diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/as/initialize-master-data.py b/core-plugin-openbis/dist/core-plugins/imaging/1/as/initialize-master-data.py
deleted file mode 100644
index e1ed0ce1fa3d472f8da523901244a6565f68343d..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/as/initialize-master-data.py
+++ /dev/null
@@ -1,73 +0,0 @@
-#
-# Copyright 2014 ETH Zuerich, Scientific IT Services
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-# MasterDataRegistrationTransaction Class
-from ch.ethz.sis.openbis.generic.server.asapi.v3 import ApplicationServerApi
-from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id import CustomASServiceCode
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.service import CustomASServiceExecutionOptions
-from ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl import MasterDataRegistrationHelper
-import sys
-
-helper = MasterDataRegistrationHelper(sys.path)
-api = CommonServiceProvider.getApplicationContext().getBean(ApplicationServerApi.INTERNAL_SERVICE_NAME)
-sessionToken = api.loginAsSystem()
-props = CustomASServiceExecutionOptions().withParameter('xls', helper.listXlsByteArrays()) \
- .withParameter('method', 'import').withParameter('zip', False).withParameter('xls_name', 'IMAGING').withParameter('update_mode', 'UPDATE_IF_EXISTS') \
- .withParameter('scripts', helper.getAllScripts())
-result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import"), props)
-api.logout(sessionToken)
-print("======================== imaging-master-data xls ingestion result ========================")
-print(result)
-print("======================== imaging-data xls ingestion result ========================")
-
-
-
-# from ch.ethz.sis.openbis.generic.server.asapi.v3 import ApplicationServerApi
-# from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
-# from ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id import CustomASServiceCode
-# from ch.ethz.sis.openbis.generic.asapi.v3.dto.service import CustomASServiceExecutionOptions
-# from ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl import MasterDataRegistrationHelper
-# import sys
-#
-# from ch.systemsx.cisd.openbis.generic.server.hotfix import ELNFixes
-# from ch.systemsx.cisd.openbis.generic.server.hotfix import ELNAnnotationsMigration
-# from ch.systemsx.cisd.openbis.generic.server.hotfix import ELNCollectionTypeMigration
-#
-# api = CommonServiceProvider.getApplicationContext().getBean(ApplicationServerApi.INTERNAL_SERVICE_NAME)
-# sessionToken = api.loginAsSystem()
-#
-# if ELNFixes.isELNInstalled():
-# ELNFixes.beforeUpgrade(sessionToken)
-# ELNAnnotationsMigration.beforeUpgrade(sessionToken)
-# ELNCollectionTypeMigration.beforeUpgrade(sessionToken)
-#
-# helper = MasterDataRegistrationHelper(sys.path)
-# props = CustomASServiceExecutionOptions().withParameter('xls', helper.getByteArray("common-data-model.xls"))\
-# .withParameter('method', 'import').withParameter('zip', False).withParameter('xls_name', 'ELN-LIMS').withParameter('update_mode', 'UPDATE_IF_EXISTS')\
-# .withParameter('scripts', helper.getAllScripts())
-# result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import"), props)
-#
-# if not ELNFixes.isMultiGroup():
-# props = CustomASServiceExecutionOptions().withParameter('xls', helper.getByteArray("single-group-data-model.xls"))\
-# .withParameter('method', 'import').withParameter('zip', False).withParameter('xls_name', 'ELN-LIMS').withParameter('update_mode', 'UPDATE_IF_EXISTS')\
-# .withParameter('scripts', helper.getAllScripts())
-# result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import"), props)
-#
-# ELNCollectionTypeMigration.afterUpgrade()
-# api.logout(sessionToken)
-# print("======================== master-data xls ingestion result ========================")
-# print(result)
-# print("======================== master-data xls ingestion result ========================")
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/imaging-data-model.xls b/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/imaging-data-model.xls
deleted file mode 100644
index 8f88765f4618a3462bf4118c977d56eb9f621c5d..0000000000000000000000000000000000000000
Binary files a/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/imaging-data-model.xls and /dev/null differ
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/scripts/imaging_dataset_config_validation.py b/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/scripts/imaging_dataset_config_validation.py
deleted file mode 100644
index 6766c2ff21171002a28224386024fbd241407c28..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/scripts/imaging_dataset_config_validation.py
+++ /dev/null
@@ -1,182 +0,0 @@
-# Copyright ETH 2023 Zürich, Scientific IT Services
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-import json
-
-
-def assert_control(control_config):
- if not control_config:
- return True, ''
- obligatory_tags = ['@type', 'label', 'type']
- for tag in obligatory_tags:
- if tag not in control_config:
- return False, tag+': is missing!'
- if control_config[tag] is None:
- return False, tag+': can not be empty!'
-
- list_tags = ['values', 'range', 'speeds', 'visibility']
- for list_tag in list_tags:
- if list_tag in control_config and control_config[list_tag] is not None and not isinstance(control_config[list_tag], list):
- return False, list_tag+': must be a list or null!'
-
- boolean_tags = ['playable', 'multiselect']
- for boolean_tag in boolean_tags:
- if boolean_tag in control_config and control_config[boolean_tag] is not None and not isinstance(control_config[boolean_tag], bool):
- return False, boolean_tag+': must be a boolean or empty!'
-
- if 'visibility' in control_config and control_config['visibility'] is not None:
- visibility = control_config['visibility']
- for vis in visibility:
- tags = ['label', 'values']
- all_tags = tags + ['range', 'unit']
- for tag in ['label', 'values']:
- if tag not in vis:
- return False, 'visibility->'+tag+': is missing!'
- if vis[tag] is None:
- return False, 'visibility->'+tag+': can not be empty!'
-
- for tag in ['values', 'range']:
- if tag in vis and vis[tag] is not None and not isinstance(vis[tag], list):
- return False, 'visibility->'+tag+': must be a list!'
-
- if 'metadata' in control_config and control_config['metadata'] is not None and not isinstance(control_config['metadata'], dict):
- return False, '->metadata: must be a dictionary or null!'
-
- return True, ''
-
-
-def assert_config(json_config):
- if 'config' in json_config:
- config = json_config['config']
- obligatory_tags = ['@type', 'adaptor', 'version', 'playable', 'exports', 'inputs']
- for tag in obligatory_tags:
- if tag not in config:
- return False, 'config->' + tag + ': is missing!'
- if config[tag] is None:
- return False, 'config->' + tag + ': can not be empty!'
-
- if config['adaptor'].strip() == '':
- return False, 'config->adaptor: can not be blank!'
-
- list_tags = ['speeds', 'resolutions', 'exports', 'inputs']
- for list_tag in list_tags:
- if list_tag in config and config[list_tag] is not None and not isinstance(config[list_tag], list):
- return False, '\''+list_tag+'\' must be a list or null!'
-
- if not isinstance(config['playable'], bool):
- return False, 'config->playable: must be a boolean!'
-
- for control in config['exports']:
- result, err = assert_control(control)
- if not result:
- return result, 'config->exports->' + err
-
- for control in config['inputs']:
- result, err = assert_control(control)
- if not result:
- return result, 'config->inputs->' + err
-
- if 'metadata' in config and config['metadata'] is not None and not isinstance(config['metadata'], dict):
- return False, 'config->metadata: must be a dictionary or null!'
- else:
- return False, 'Missing \'config\' tag in configuration!'
- return True, ''
-
-
-def assert_preview(preview_config):
- obligatory_tags = ['@type', 'format', 'show']
- for tag in obligatory_tags:
- if tag not in config:
- return False, tag + ': is missing!'
- if config[tag] is None:
- return False, tag + ': can not be empty!'
-
- if not isinstance(preview_config['show'], bool):
- return False, 'show: must be boolean!'
-
- if not isinstance(preview_config['format'], str):
- return False, 'format: must be string!'
-
- if 'bytes' in preview_config and preview_config['bytes'] is not None and not isinstance(preview_config['bytes'], str):
- return False, 'bytes: must be a base64 encoded string or null!'
-
- if 'metadata' in preview_config and preview_config['metadata'] is not None and not isinstance(preview_config['metadata'], dict):
- return False, 'metadata: must be a dictionary or null!'
-
- if 'config' in preview_config and preview_config['config'] is not None and not isinstance(preview_config['config'], dict):
- return False, 'config: must be a dictionary or null!'
-
- return True, ''
-
-
-def assert_images(json_config):
- if 'images' in json_config:
- images = json_config['images']
- if images is None:
- return False, '\'images\' tag can not be null!'
- if not isinstance(images, list):
- return False, '\'images\' tag must be a list!'
-
- for image in images:
- obligatory_tags = ['@type']
- for tag in obligatory_tags:
- if tag not in image:
- return False, 'images->' + tag + ': missing tag!'
- if image[tag] is None:
- return False, 'images->' + tag + ': can not be empty!'
-
- if 'metadata' in image and image['metadata'] is not None and not isinstance(image['metadata'], dict):
- return False, 'images->metadata: must be a dictionary or null!'
-
- if 'previews' in image and image['previews'] is not None and not isinstance(image['previews'], list):
- return False, 'images->previews: must be a list or null!'
-
- for preview in image['previews']:
- res, err = assert_preview(preview)
- if not res:
- return result, 'images->previews->' + err
-
- else:
- return False, 'Missing \'images\' tag in configuration!'
- return True, ''
-
-
-def get_rendered_property(entity, property):
- properties = entity.externalDataPE().getProperties()
- for prop in properties:
- etpt = prop.getEntityTypePropertyType()
- pt = etpt.getPropertyType()
- code = pt.getCode()
- if code == property:
- return prop.tryGetUntypedValue()
- return None
-
-
-def validate(entity, is_new):
- imaging_dataset_config = get_rendered_property(entity, "$IMAGING_DATA_CONFIG")
- if imaging_dataset_config is None or imaging_dataset_config == "":
- return "Imaging dataset config can not be empty!"
- elif "test_validation_failure" in imaging_dataset_config:
- return "Imaging dataset config validation failure!"
- else:
-
- try:
- config = json.loads(imaging_dataset_config)
- except Exception as e:
- return "Could not parse JSON: " + e
-
- result, err = assert_config(config)
- if not result:
- return err
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/openBIS-premise-imaging.jar b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/openBIS-premise-imaging.jar
deleted file mode 100644
index 4b4684b9fca92f5c299aa0ac081570eae50770bb..0000000000000000000000000000000000000000
Binary files a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/openBIS-premise-imaging.jar and /dev/null differ
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/build.gradle b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/build.gradle
deleted file mode 100644
index 0f364e5221162812c2b0f0e7de1b132145701821..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/build.gradle
+++ /dev/null
@@ -1,59 +0,0 @@
-apply from: 'javaproject.gradle'
-apply from: 'repository.gradle'
-
-//evaluationDependsOn(':api-openbis-java')
-
-dependencies {
- api project(':api-openbis-java'),
- project(':server-original-data-store')
-
- implementation 'fasterxml:jackson-annotations:2.9.10',
- 'fasterxml:jackson-core:2.9.10',
- 'fasterxml:jackson-databind:2.9.10.8',
- 'fasterxml:jackson-datatype-jsr310:2.9.10'
-
-// testImplementation 'testng:testng:6.8-CISD'
-// project(':server-original-data-store')
-
- testImplementation 'junit:junit:4.10',
- 'testng:testng:6.8-CISD'
-
- testRuntimeOnly 'hamcrest:hamcrest-core:1.3',
- project(':server-original-data-store')
-}
-
-sourceSets {
- main {
- resources {
- srcDirs = ['source/java/*']
- }
- }
- test {
- resources {
- srcDirs = ['sourceTest/java']
- }
- }
-}
-
-//test {
-// workingDir = '.'
-//}
-
-def premiseArchiveName = 'openBIS-premise-imaging.jar'
-jar {
- dependsOn compileJava
- archiveName premiseArchiveName
- includeEmptyDirs false
-}
-
-
-task premiseImagingJar(type: Copy) {
- dependsOn jar
- from("${project.buildDir}/libs/${premiseArchiveName}")
- into ".."
- doLast {
-// delete "${project.buildDir}/${premiseArchiveName}"
-// delete "${project.buildDir}"
-// delete
- }
-}
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradle/wrapper/gradle-wrapper.jar b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradle/wrapper/gradle-wrapper.jar
deleted file mode 100644
index 5c2d1cf016b3885f6930543d57b744ea8c220a1a..0000000000000000000000000000000000000000
Binary files a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradle/wrapper/gradle-wrapper.jar and /dev/null differ
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradle/wrapper/gradle-wrapper.properties b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradle/wrapper/gradle-wrapper.properties
deleted file mode 100644
index 7745c4ec463c7bb1c4ff6a5e58db239890345152..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradle/wrapper/gradle-wrapper.properties
+++ /dev/null
@@ -1,5 +0,0 @@
-distributionBase=GRADLE_USER_HOME
-distributionPath=wrapper/dists
-distributionUrl=https\://sissource.ethz.ch/openbis/openbis-public/openbis-ivy/-/raw/main/gradle/distribution/7.4/gradle-7.4-bin.zip
-zipStoreBase=GRADLE_USER_HOME
-zipStorePath=wrapper/dists
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradlew b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradlew
deleted file mode 100755
index 83f2acfdc319a24e8766cca78f32474ad7a22dd6..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradlew
+++ /dev/null
@@ -1,188 +0,0 @@
-#!/usr/bin/env sh
-
-#
-# Copyright 2015 the original author or authors.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# https://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-##############################################################################
-##
-## Gradle start up script for UN*X
-##
-##############################################################################
-
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
- ls=`ls -ld "$PRG"`
- link=`expr "$ls" : '.*-> \(.*\)$'`
- if expr "$link" : '/.*' > /dev/null; then
- PRG="$link"
- else
- PRG=`dirname "$PRG"`"/$link"
- fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
-
-# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
-
-warn () {
- echo "$*"
-}
-
-die () {
- echo
- echo "$*"
- echo
- exit 1
-}
-
-# OS specific support (must be 'true' or 'false').
-cygwin=false
-msys=false
-darwin=false
-nonstop=false
-case "`uname`" in
- CYGWIN* )
- cygwin=true
- ;;
- Darwin* )
- darwin=true
- ;;
- MINGW* )
- msys=true
- ;;
- NONSTOP* )
- nonstop=true
- ;;
-esac
-
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
-
-# Determine the Java command to use to start the JVM.
-if [ -n "$JAVA_HOME" ] ; then
- if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
- # IBM's JDK on AIX uses strange locations for the executables
- JAVACMD="$JAVA_HOME/jre/sh/java"
- else
- JAVACMD="$JAVA_HOME/bin/java"
- fi
- if [ ! -x "$JAVACMD" ] ; then
- die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
- fi
-else
- JAVACMD="java"
- which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
-fi
-
-# Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
- MAX_FD_LIMIT=`ulimit -H -n`
- if [ $? -eq 0 ] ; then
- if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
- MAX_FD="$MAX_FD_LIMIT"
- fi
- ulimit -n $MAX_FD
- if [ $? -ne 0 ] ; then
- warn "Could not set maximum file descriptor limit: $MAX_FD"
- fi
- else
- warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
- fi
-fi
-
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
- GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
-
-# For Cygwin or MSYS, switch paths to Windows format before running java
-if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
- APP_HOME=`cygpath --path --mixed "$APP_HOME"`
- CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
- JAVACMD=`cygpath --unix "$JAVACMD"`
-
- # We build the pattern for arguments to be converted via cygpath
- ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
- SEP=""
- for dir in $ROOTDIRSRAW ; do
- ROOTDIRS="$ROOTDIRS$SEP$dir"
- SEP="|"
- done
- OURCYGPATTERN="(^($ROOTDIRS))"
- # Add a user-defined pattern to the cygpath arguments
- if [ "$GRADLE_CYGPATTERN" != "" ] ; then
- OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
- fi
- # Now convert the arguments - kludge to limit ourselves to /bin/sh
- i=0
- for arg in "$@" ; do
- CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
- CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
-
- if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
- eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
- else
- eval `echo args$i`="\"$arg\""
- fi
- i=$((i+1))
- done
- case $i in
- (0) set -- ;;
- (1) set -- "$args0" ;;
- (2) set -- "$args0" "$args1" ;;
- (3) set -- "$args0" "$args1" "$args2" ;;
- (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
- (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
- (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
- (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
- (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
- (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
- esac
-fi
-
-# Escape application args
-save () {
- for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
- echo " "
-}
-APP_ARGS=$(save "$@")
-
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
-
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
- cd "$(dirname "$0")"
-fi
-
-exec "$JAVACMD" "$@"
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradlew.bat b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradlew.bat
deleted file mode 100644
index 9618d8d9607cd91a0efb866bcac4810064ba6fac..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/gradlew.bat
+++ /dev/null
@@ -1,100 +0,0 @@
-@rem
-@rem Copyright 2015 the original author or authors.
-@rem
-@rem Licensed under the Apache License, Version 2.0 (the "License");
-@rem you may not use this file except in compliance with the License.
-@rem You may obtain a copy of the License at
-@rem
-@rem https://www.apache.org/licenses/LICENSE-2.0
-@rem
-@rem Unless required by applicable law or agreed to in writing, software
-@rem distributed under the License is distributed on an "AS IS" BASIS,
-@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-@rem See the License for the specific language governing permissions and
-@rem limitations under the License.
-@rem
-
-@if "%DEBUG%" == "" @echo off
-@rem ##########################################################################
-@rem
-@rem Gradle startup script for Windows
-@rem
-@rem ##########################################################################
-
-@rem Set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" setlocal
-
-set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
-set APP_BASE_NAME=%~n0
-set APP_HOME=%DIRNAME%
-
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
-
-@rem Find java.exe
-if defined JAVA_HOME goto findJavaFromJavaHome
-
-set JAVA_EXE=java.exe
-%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
-
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:findJavaFromJavaHome
-set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-
-if exist "%JAVA_EXE%" goto init
-
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
-:execute
-@rem Setup the command line
-
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
-
-@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
-
-:end
-@rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
-
-:fail
-rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
-rem the _cmd.exe /c_ return code!
-if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
-
-:mainEnd
-if "%OS%"=="Windows_NT" endlocal
-
-:omega
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/javaproject.gradle b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/javaproject.gradle
deleted file mode 100644
index 82beac14965d9eac35b897c9be2a26e2ff3cb54f..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/javaproject.gradle
+++ /dev/null
@@ -1,412 +0,0 @@
-apply plugin: 'java-library'
-apply plugin: 'project-report'
-
-evaluationDependsOnChildren()
-
-configurations {
- implementation {
- canBeResolved = true
- }
- testImplementation {
- canBeResolved = true
- }
- runtimeOnly {
- canBeResolved = true
- }
- tests.extendsFrom testRuntimeOnly
-}
-
-configurations {
- ecj
-}
-
-configurations.all {
- resolutionStrategy.cacheDynamicVersionsFor 0, 'hours'
- resolutionStrategy.cacheChangingModulesFor 0, 'hours'
-}
-
-//task wrapper(type: Wrapper) {
-// gradleVersion = '4.10.3'
-// distributionUrl = "https://services.gradle.org/distributions/gradle-4.10.3-bin.zip"
-//}
-sourceCompatibility='11'
-targetCompatibility='11'
-
-sourceSets {
- main {
- java {
- srcDirs = ['source/java']
- }
- }
- test {
- java {
- srcDirs = ['sourceTest/java']
- }
- resources {
- srcDirs = ['sourceTest/java']
- }
- }
- examples {
- java {
- srcDirs = ['sourceExamples/java']
- }
- }
-}
-
-buildDir = 'targets/gradle'
-
-buildscript {
- apply from: './repository.gradle'
-
- repositories repositoryConfig
-
- dependencies {
- classpath 'cisd:cisd-ant-tasks:r29834'
- }
-}
-
-repositories repositoryConfig
-
-def execute(command, arguments) {
- new ByteArrayOutputStream().withStream { os ->
- print "execute: ${command}"
- arguments.collect({print " ${it}"})
- println ''
- def result = exec {
- executable = command
- args = arguments
- standardOutput = os
- }
- return os.toString().split('\n')
- }
-}
-
-ext.executeFunction = {
- command, arguments -> execute(command, arguments)
-}
-
-def execute_working_dir(command, arguments, working_dir) {
- new ByteArrayOutputStream().withStream { os ->
- print "execute: ${command}"
- arguments.collect({print " ${it}"})
- println ''
- def result = exec {
- executable = command
- args = arguments
- standardOutput = os
- }
- return os.toString().split('\n')
- }
-}
-
-ext.svnCommand = 'svn'
-
-def isSvnProject() {
- return new java.io.File(projectDir, ".svn").isDirectory() || new java.io.File(projectDir, "../.svn").isDirectory()
-}
-
-def isGitProject() {
- return new java.io.File(projectDir, ".git").isDirectory() || new java.io.File(projectDir, "../.git").isDirectory()
-}
-
-def executeSVN(arguments) {
- arguments.add(0, '--non-interactive')
- return execute(svnCommand, arguments)
-}
-
-def calculateCleanFlag() {
- return 'clean'
- for (childProject in project.childProjects.values()) {
- if (childProject.cleanFlag == 'dirty') {
- return 'dirty'
- }
- }
- def isSvn = isSvnProject()
- if (isSvn) {
- def output = executeSVN(['status', '../' + project.name])
- def lines = output.findAll({ (it.startsWith('?') || it.trim().isEmpty()) == false})
- return lines.isEmpty() ? 'clean' : 'dirty'
- } else if (isGitProject()) {
- def output = execute_working_dir('git', ['status', '--porcelain'], '../' + project.name)
- return output.length == 0 ? 'clean' : 'dirty'
- } else {
- return 'dirty'
- }
-}
-
-def findMaximum(lines, key) {
- return lines.findAll({ it.startsWith(key)}).collect({element -> element.split(':')[1].toInteger()}).max()
-}
-
-def calculateBuildInfo() {
- if (isSvnProject()) {
- def output = executeSVN(['info', '-R', '../' + project.name])
- def maxRevisionNumber = findMaximum(output, 'Revision:')
- project.ext.revisionNumber = findMaximum(output, 'Last Changed Rev:')
- if (maxRevisionNumber < project.ext.revisionNumber) {
- throw new GradleException("Maximum revision ($maxRevisionNumber) is less than the maximum "
- + "last changed revision ($project.ext.revisionNumber).")
- }
- project.ext.versionNumber = 'SNAPSHOT'
- def url = output.findAll({ it.startsWith('URL:')})[0].split('URL:')[1].trim()
- if (url.contains('/trunk') == false) {
- def pathElements = url.split('/')
- project.ext.versionNumber = 'libraries' == pathElements[-2] ? pathElements[-3] : pathElements[-2]
- }
- } else if (isGitProject()) {
- def gitlogoutput = execute_working_dir('git', ['log', '-1', '--format=%at'], '../' + project.name)
- project.ext.revisionNumber = Integer.parseInt(gitlogoutput[0])
- def tag = 'git tag -l --points-at HEAD'.execute().text.trim()
- if (tag == null || tag.isEmpty() || tag.contains('pybis')) {
- project.ext.versionNumber = 'SNAPSHOT'
- } else {
- project.ext.versionNumber = tag
- }
- } else {
- project.ext.revisionNumber = 1
- project.ext.versionNumber = 'SNAPSHOT'
- }
-
- for (childProject in project.childProjects.values()) {
- project.ext.revisionNumber = Math.max(project.ext.revisionNumber, childProject.revisionNumber)
- if (project.ext.versionNumber != childProject.versionNumber) {
- throw new GradleException("Inconsistent version numbers: "
- + "${project.name} at version ${project.ext.versionNumber} but "
- + "${childProject.name} at version ${childProject.versionNumber}.")
- }
- }
- version = "${project.ext.versionNumber}-r${project.ext.revisionNumber}"
- project.ext.revisionForPublication = project.ext.versionNumber.startsWith('SNAPSHOT') ? "r${project.ext.revisionNumber}" : project.ext.versionNumber
- project.ext.cleanFlag = calculateCleanFlag()
-
- def buildInfo = "${project.ext.versionNumber}:${project.ext.revisionNumber}:${project.ext.cleanFlag}"
- def buildInfoDev = "${project.ext.versionNumber}-dev:${project.ext.revisionNumber}:${project.ext.cleanFlag}"
-
- println "BUILD INFO for $project: $buildInfo"
-
- def targetsDistFolder = new File("${project.projectDir}/targets/dist")
- targetsDistFolder.deleteDir()
- targetsDistFolder.mkdirs()
-
- def targetDistBuildInfo = new File(targetsDistFolder, "BUILD-${project.name}.INFO")
- targetDistBuildInfo << buildInfo
-
- def mainClassesFolder = new File("${project.projectDir}/targets/gradle/classes/java/main")
- mainClassesFolder.mkdirs()
-
- def mainClassesBuildInfo = new File(mainClassesFolder, "BUILD-${project.name}.INFO")
- mainClassesBuildInfo.delete()
- mainClassesBuildInfo << buildInfoDev
-}
-
-calculateBuildInfo()
-
-group='cisd'
-
-task checkRestrictions(type: Exec, dependsOn: [classes, testClasses]) {
- doFirst {
-/*
- def cp = configurations.testImplementation.filter({ f -> f.name.startsWith('restrictionchecker') || f.name.startsWith('bcel')}).asPath
- def cmd = ['java', '-cp', cp, 'ch.rinn.restrictions.RestrictionChecker', '-r', sourceSets.main.output.classesDirs.first()]
- if (sourceSets.test.output.classesDirs.first().exists()) {
- cmd.add(sourceSets.test.output.classesDirs.first())
- }
- cmd.add('-cp')
- cmd.add(sourceSets.main.output.classesDirs.first())
- if (sourceSets.test.output.classesDirs.first().exists()) {
- cmd.add(sourceSets.test.output.classesDirs.first())
- }
- cmd.add(configurations.testImplementation.asPath)
- commandLine cmd
-*/
- commandLine = ['pwd']
- }
-}
-
-def deleteSymbolicLinksRecursively(file) {
- def absolutePath = file.getAbsolutePath()
- def canonicalPath = file.getCanonicalPath()
- if (absolutePath.equals(canonicalPath) == false) {
- file.delete();
- } else if (file.isDirectory()) {
- File[] files = file.listFiles()
- for (File child : files) {
- deleteSymbolicLinksRecursively(child)
- }
- }
-}
-
-task deleteSymLinks {
- doFirst {
- println "DELETE SYM LINKS in $buildDir"
- deleteSymbolicLinksRecursively buildDir
- }
-}
-
-clean.dependsOn deleteSymLinks
-
-test {
- useTestNG()
- options.suites('sourceTest/java/tests.xml')
-
- systemProperty "ant.project.name", project.name
-
- maxHeapSize = "8192m"
- jvmArgs '-Duser.timezone=Europe/Zurich', '-Dorg.eclipse.jetty.util.log.class=org.eclipse.jetty.util.log.StrErrLog'
-
- testLogging.showStandardStreams = true
- ignoreFailures = true
-}
-test.dependsOn checkRestrictions
-
-// Legacy Java 8 compiler from eclipse
-dependencies {
- ecj "eclipse:ecj:4.6.1"
-}
-
-if(System.getProperty("java.version").startsWith("1.8.")) {
- tasks.withType(JavaCompile) {
- options.headerOutputDirectory.convention(null)
- }
-}
-
-compileJava {
- options.encoding = 'utf-8'
- options.fork = true
- doFirst {
- // Use the legacy Java 8 compiler from eclipse for Java 8
- if(System.getProperty("java.version").startsWith("1.8.")) {
- options.forkOptions.with {
- executable = 'java'
- jvmArgs = createEclipseJDK8Args()
- }
- } else if(System.getProperty("java.version").startsWith("11.") || System.getProperty("java.version").startsWith("17.")) {
- // Use modern openJDK 11 or 17 Compiler
- } else {
- throw new Exception("Unsupported Java version found: '" + System.getProperty("java.version") + "', please use JDK8, JDK11 or JDK17");
- }
- }
-}
-
-compileTestJava {
- options.encoding = 'utf-8'
- options.fork = true
- doFirst {
- // Use the legacy Java 8 compiler from eclipse for Java 8
- if(System.getProperty("java.version").startsWith("1.8.")) {
- options.forkOptions.with {
- executable = 'java'
- jvmArgs = createEclipseJDK8Args()
- }
- } else if(System.getProperty("java.version").startsWith("11.") || System.getProperty("java.version").startsWith("17.")) {
- // Use modern openJDK 11 or 17 Compiler
- } else {
- throw new Exception("Unsupported Java version found: '" + System.getProperty("java.version") + "', please use JDK8, JDK11 or JDK17");
- }
- }
-}
-
-def createEclipseJDK8Args() {
- def args = ['-cp', configurations.ecj.asPath, 'org.eclipse.jdt.internal.compiler.batch.Main', '-nowarn']
- return args
-}
-
-processTestResources {
- fileMode=0666
-}
-
-apply plugin: 'eclipse'
-
-eclipse {
- classpath {
- downloadSources=true
- defaultOutputDir = file('targets/classes')
- }
-}
-
-eclipse.classpath.file {
- whenMerged{ classpath ->
- def projectRefs = classpath.entries.findAll{entry -> entry.kind =='src' && entry.path.startsWith('/')}
- classpath.entries.removeAll(projectRefs)
- classpath.entries.addAll(projectRefs)
- }
-}
-
-task testJar(type: Jar, dependsOn: testClasses) {
- baseName = "test-${project.archivesBaseName}"
- from sourceSets.test.output
-}
-
-task sourcesJar(type: Jar) {
- duplicatesStrategy 'include'
- classifier = 'sources'
- from sourceSets.main.allSource
-}
-
-compileJava.dependsOn sourcesJar
-
-artifacts {
- tests testJar
-}
-
-artifacts {
- archives sourcesJar
-}
-
-task compileDependencies(type: Copy) {
- into "$buildDir/output/compile-dependencies"
- from configurations.implementation
-}
-
-task runtimeDependencies(type: Copy) {
- into "$buildDir/output/runtime-dependencies"
- from configurations.runtimeOnly
-}
-
-task testCompileDependencies(type: Copy) {
- into "$buildDir/output/testCompile-dependencies"
- from configurations.testImplementation
-}
-
-task testRuntimeDependencies(type: Copy) {
- into "$buildDir/output/testRuntime-dependencies"
- from configurations.testRuntimeOnly
-}
-
-task checkDependencies(dependsOn: classes) {
- doLast {
- ant.taskdef(name: 'dependencychecker', classname: 'classycle.ant.DependencyCheckingTask', classpath: configurations.testRuntime.asPath)
- ant.dependencychecker(
- definitionFile: 'resource/dependency-structure.ddf',
- failOnUnwantedDependencies: 'true',
- mergeInnerClasses: 'true') {
- fileset(dir: "${buildDir}", includes: "**/*.class")
- }
- }
-}
-
-apply plugin: 'ivy-publish'
-if (hasProperty('ivyRepository') == false || ''.equals(project.ivyRepository))
-{
- project.ext.ivyRepository = "${project.projectDir}/../ivy-repository"
-}
-publishing {
-
- repositories {
- ivy {
- ivyPattern "file://${project.ivyRepository}/[organisation]/[module]/[revision]/ivy.xml"
- artifactPattern "file://${project.ivyRepository}/[organisation]/[module]/[revision]/[artifact]-[revision](-[classifier]).[ext]"
- }
- }
-}
-
-publish {
- dependsOn build
-}
-
-if (JavaVersion.current().isJava8Compatible()) {
- tasks.withType(Javadoc) {
- options.addStringOption('Xdoclint:none', '-quiet')
- options.addStringOption('encoding', 'utf-8')
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/repository.gradle b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/repository.gradle
deleted file mode 100644
index 1672a54cfb7dfe17c5369ae440228f76f117e29f..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/repository.gradle
+++ /dev/null
@@ -1,6 +0,0 @@
-ext.repositoryConfig = {
- ivy {
- ivyPattern "https://sissource.ethz.ch/openbis/openbis-public/openbis-ivy/-/raw/main/[organisation]/[module]/[revision]/ivy.xml"
- artifactPattern "https://sissource.ethz.ch/openbis/openbis-public/openbis-ivy/-/raw/main/[organisation]/[module]/[revision]/[artifact]-[revision](-[classifier]).[ext]"
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/settings.gradle b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/settings.gradle
deleted file mode 100644
index 0abc667a6661bc3dc5205baaeb3696a474efda62..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/settings.gradle
+++ /dev/null
@@ -1,21 +0,0 @@
-//includeFlat 'lib-commonbase', 'lib-common', 'api-openbis-java', 'lib-openbis-common', 'lib-authentication', 'lib-dbmigration', 'server-application-server',
-// 'server-original-data-store', 'server-screening', 'server-external-data-store',
-// 'ui-admin', 'lib-microservice-server', 'ui-eln-lims', 'api-openbis-javascript'
-//
-//def includes = ['lib-commonbase', 'lib-common', 'api-openbis-java', 'lib-openbis-common', 'api-openbis-javascript',
-// 'lib-authentication', 'lib-dbmigration', 'server-application-server', 'server-original-data-store']
-//
-//includes.forEach { name ->
-// includeFlat(name)
-// project(":${name}").projectDir = new File("../openbis/${name}")
-//}
-
-def includes = ['lib-common', 'lib-commonbase', 'api-openbis-java',
-'api-openbis-javascript', 'lib-openbis-common', 'lib-dbmigration', 'lib-authentication',
-'server-original-data-store', 'server-application-server'
-]
-
-includes.forEach { name ->
- includeFlat(name)
- project(":${name}").projectDir = new File("../../../../../../../../../../${name}")
-}
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/PingPongService.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/PingPongService.java
deleted file mode 100644
index ae4934db548a3dec51d7b352a6a60c6a09fb26d1..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/PingPongService.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins;
-
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.CustomDSSServiceExecutionOptions;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.id.ICustomDSSServiceId;
-import ch.ethz.sis.openbis.generic.dssapi.v3.plugin.service.ICustomDSSServiceExecutor;
-
-import java.io.Serializable;
-import java.util.Map;
-import java.util.Properties;
-
-public class PingPongService implements ICustomDSSServiceExecutor
-{
- public PingPongService(Properties properties)
- {
- System.out.println("||> INIT PING PONG SERVICE");
- }
- @Override
- public Serializable executeService(String sessionToken, ICustomDSSServiceId serviceId,
- CustomDSSServiceExecutionOptions options)
- {
- Map<String, Object> params = options.getParameters();
- if(params.containsKey("key") && params.get("key").toString().equalsIgnoreCase("PING"))
- {
- return "PONG";
- }
- throw new IllegalArgumentException("Missing Ping parameter");
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetConfig.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetConfig.java
deleted file mode 100644
index 7ce7ed60b56e81ba8617b11eefda81e9ce642505..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetConfig.java
+++ /dev/null
@@ -1,153 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
-
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import java.io.Serializable;
-import java.util.List;
-import java.util.Map;
-
-@JsonObject("dss.dto.imaging.ImagingDataSetConfig")
-public class ImagingDataSetConfig implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
-
- @JsonProperty
- private String adaptor;
-
- @JsonProperty
- private Double version;
-
- @JsonProperty
- private List<Integer> speeds;
-
- @JsonProperty
- private List<String> resolutions;
-
- @JsonProperty
- private boolean playable;
-
- @JsonProperty
- private List<ImagingDataSetControl> exports;
-
- @JsonProperty
- private List<ImagingDataSetControl> inputs;
-
- @JsonProperty
- private Map<String, String> metaData;
-
- @JsonIgnore
- public String getAdaptor()
- {
- return adaptor;
- }
-
- public void setAdaptor(String adaptor)
- {
- this.adaptor = adaptor;
- }
-
- @JsonIgnore
- public Double getVersion()
- {
- return version;
- }
-
- public void setVersion(Double version)
- {
- this.version = version;
- }
-
- @JsonIgnore
- public List<Integer> getSpeeds()
- {
- return speeds;
- }
-
- public void setSpeeds(List<Integer> speeds)
- {
- this.speeds = speeds;
- }
-
- @JsonIgnore
- public List<String> getResolutions()
- {
- return resolutions;
- }
-
- public void setResolutions(List<String> resolutions)
- {
- this.resolutions = resolutions;
- }
-
- @JsonIgnore
- public boolean isPlayable()
- {
- return playable;
- }
-
- public void setPlayable(boolean playable)
- {
- this.playable = playable;
- }
-
- @JsonIgnore
- public List<ImagingDataSetControl> getExports()
- {
- return exports;
- }
-
- public void setExports(
- List<ImagingDataSetControl> exports)
- {
- this.exports = exports;
- }
-
- @JsonIgnore
- public List<ImagingDataSetControl> getInputs()
- {
- return inputs;
- }
-
- public void setInputs(
- List<ImagingDataSetControl> inputs)
- {
- this.inputs = inputs;
- }
-
- @JsonIgnore
- public Map<String, String> getMetaData()
- {
- return metaData;
- }
-
- public void setMetaData(Map<String, String> metaData)
- {
- this.metaData = metaData;
- }
-
- @Override
- public String toString()
- {
- return "ImagingDataSetConfig: " + adaptor;
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControl.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControl.java
deleted file mode 100644
index 7d5c27fe9ce8562ced6418828f8734a80d90e365..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControl.java
+++ /dev/null
@@ -1,192 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
-
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import java.io.Serializable;
-import java.util.List;
-import java.util.Map;
-
-@JsonObject("dss.dto.imaging.ImagingDataSetControl")
-public class ImagingDataSetControl implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @JsonProperty
- private String label;
-
- @JsonProperty
- private String section;
-
- @JsonProperty
- private String type;
-
- @JsonProperty
- private List<String> values;
-
- @JsonProperty
- private String unit;
-
- @JsonProperty
- private List<String> range;
-
- @JsonProperty
- private boolean multiselect;
-
- @JsonProperty
- private Boolean playable;
-
- @JsonProperty
- private List<Integer> speeds;
- @JsonProperty
- private List<ImagingDataSetControlVisibility> visibility;
-
- @JsonProperty
- private Map<String, String> metaData;
-
- @JsonIgnore
- public String getLabel()
- {
- return label;
- }
-
- public void setLabel(String label)
- {
- this.label = label;
- }
-
- @JsonIgnore
- public String getSection()
- {
- return section;
- }
-
- public void setSection(String section)
- {
- this.section = section;
- }
-
- @JsonIgnore
- public String getUnit()
- {
- return unit;
- }
-
- public void setUnit(String unit)
- {
- this.unit = unit;
- }
-
- @JsonIgnore
- public String getType()
- {
- return type;
- }
-
- public void setType(String type)
- {
- this.type = type;
- }
-
- @JsonIgnore
- public List<String> getValues()
- {
- return values;
- }
-
- public void setValues(List<String> values)
- {
- this.values = values;
- }
-
- @JsonIgnore
- public boolean isMultiselect()
- {
- return multiselect;
- }
-
- public void setMultiselect(boolean multiselect)
- {
- this.multiselect = multiselect;
- }
-
- @JsonIgnore
- public Boolean getPlayable()
- {
- return playable;
- }
-
- public void setPlayable(Boolean playable)
- {
- this.playable = playable;
- }
-
- @JsonIgnore
- public List<Integer> getSpeeds()
- {
- return speeds;
- }
-
- public void setSpeeds(List<Integer> speeds)
- {
- this.speeds = speeds;
- }
-
- @JsonIgnore
- public List<String> getRange()
- {
- return range;
- }
-
- public void setRange(List<String> range)
- {
- this.range = range;
- }
-
- @JsonIgnore
- public List<ImagingDataSetControlVisibility> getVisibility()
- {
- return visibility;
- }
-
- public void setVisibility(
- List<ImagingDataSetControlVisibility> visibility)
- {
- this.visibility = visibility;
- }
-
- @JsonIgnore
- public Map<String, String> getMetaData()
- {
- return metaData;
- }
-
- public void setMetaData(Map<String, String> metaData)
- {
- this.metaData = metaData;
- }
-
- @Override
- public String toString()
- {
- return "ImagingDataSetControl: " + label;
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControlVisibility.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControlVisibility.java
deleted file mode 100644
index 2a364ad0745a2c5f8205090e428b27662bbaa792..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControlVisibility.java
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
-
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import java.io.Serializable;
-import java.util.List;
-
-@JsonObject("dss.dto.imaging.ImagingDataSetControlVisibility")
-public class ImagingDataSetControlVisibility implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @JsonProperty
- private String label;
- @JsonProperty
- private List<String> values;
- @JsonProperty
- private List<String> range;
- @JsonProperty
- private String unit;
-
- @JsonIgnore
- public String getLabel()
- {
- return label;
- }
-
- public void setLabel(String label)
- {
- this.label = label;
- }
- @JsonIgnore
- public List<String> getValues()
- {
- return values;
- }
-
- public void setValues(List<String> values)
- {
- this.values = values;
- }
- @JsonIgnore
- public List<String> getRange()
- {
- return range;
- }
-
- public void setRange(List<String> range)
- {
- this.range = range;
- }
-
- @JsonIgnore
- public String getUnit()
- {
- return unit;
- }
-
- public void setUnit(String unit)
- {
- this.unit = unit;
- }
-
- @Override
- public String toString()
- {
- return "ImagingDataSetControlVisibility: " + label;
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java
deleted file mode 100644
index 8d46949ea194fead71a42248edc6e3ccbcc75025..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.property.PropertiesDeserializer;
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
-
-import java.io.Serializable;
-import java.util.Map;
-
-@JsonObject("dss.dto.imaging.ImagingDataSetExport")
-public class ImagingDataSetExport implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @JsonProperty
- @JsonDeserialize(contentUsing = PropertiesDeserializer.class)
- private Map<String, Serializable> config;
-
- @JsonProperty
- @JsonDeserialize(contentUsing = PropertiesDeserializer.class)
- private Map<String, String> metaData;
-
- @JsonIgnore
- public Map<String, Serializable> getConfig()
- {
- return config;
- }
-
- public void setConfig(Map<String, Serializable> config)
- {
- this.config = config;
- }
-
- @JsonIgnore
- public Map<String, String> getMetaData()
- {
- return metaData;
- }
-
- public void setMetaData(Map<String, String> metaData)
- {
- this.metaData = metaData;
- }
-
- @Override
- public String toString()
- {
- return "ImagingDataSetExport";
- }
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java
deleted file mode 100644
index e726231d0e42141dd27912cffa0dd75b9e6b497c..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java
+++ /dev/null
@@ -1,81 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
-
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import java.io.Serializable;
-import java.util.List;
-import java.util.Map;
-
-@JsonObject("dss.dto.imaging.ImagingDataSetImage")
-public class ImagingDataSetImage implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @JsonProperty
- private List<ImagingDataSetPreview> previews;
-
- @JsonProperty
- private Map<String, Serializable> config;
-
- @JsonProperty
- private Map<String, String> metaData;
-
- @JsonIgnore
- public List<ImagingDataSetPreview> getPreviews()
- {
- return previews;
- }
-
- public void setPreviews(
- List<ImagingDataSetPreview> previews)
- {
- this.previews = previews;
- }
-
- public Map<String, Serializable> getConfig()
- {
- return config;
- }
-
- public void setConfig(Map<String, Serializable> config)
- {
- this.config = config;
- }
-
- @JsonIgnore
- public Map<String, String> getMetaData()
- {
- return metaData;
- }
-
- public void setMetaData(Map<String, String> metaData)
- {
- this.metaData = metaData;
- }
-
- @Override
- public String toString()
- {
- return "ImagingDataSetImage:";
- }
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetMultiExport.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetMultiExport.java
deleted file mode 100644
index d46ced3b5a06b2cbf46a7bb28748ed7f6955d9fd..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetMultiExport.java
+++ /dev/null
@@ -1,97 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
-
-
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.property.PropertiesDeserializer;
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
-
-import java.io.Serializable;
-import java.util.List;
-import java.util.Map;
-
-@JsonObject("dss.dto.imaging.ImagingDataSetMultiExport")
-public class ImagingDataSetMultiExport implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @JsonProperty
- private String permId;
- @JsonProperty
- private int index;
-
- @JsonProperty
- @JsonDeserialize(contentUsing = PropertiesDeserializer.class)
- private Map<String, Serializable> config;
-
- @JsonProperty
- @JsonDeserialize(contentUsing = PropertiesDeserializer.class)
- private Map<String, String> metaData;
-
- @JsonIgnore
- public String getPermId()
- {
- return permId;
- }
-
- public void setPermId(String permId) {
- this.permId = permId;
- }
-
- @JsonIgnore
- public int getIndex()
- {
- return index;
- }
-
- public void setIndex(int index) {
- this.index = index;
- }
-
- @JsonIgnore
- public Map<String, Serializable> getConfig()
- {
- return config;
- }
-
- public void setConfig(Map<String, Serializable> config)
- {
- this.config = config;
- }
-
- @JsonIgnore
- public Map<String, String> getMetaData()
- {
- return metaData;
- }
-
- public void setMetaData(Map<String, String> metaData)
- {
- this.metaData = metaData;
- }
-
- @Override
- public String toString()
- {
- return "ImagingDataSetMultiExport:" + permId;
- }
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPreview.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPreview.java
deleted file mode 100644
index 39e85e507c7e95387897dcfd9c7f136f5f3f273a..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPreview.java
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.property.PropertiesDeserializer;
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
-
-import java.io.Serializable;
-import java.util.List;
-import java.util.Map;
-
-@JsonObject("dss.dto.imaging.ImagingDataSetPreview")
-public class ImagingDataSetPreview implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @JsonProperty
- @JsonDeserialize(contentUsing = PropertiesDeserializer.class)
- private Map<String, Serializable> config;
-
- @JsonProperty
- private String format;
-
- @JsonProperty
- private String bytes;
-
- @JsonProperty
- private boolean show;
-
- @JsonProperty
- private Map<String, String> metaData;
-
-
- @JsonIgnore
- public Map<String, Serializable> getConfig()
- {
- return config;
- }
-
- public void setConfig(Map<String, Serializable> config)
- {
- this.config = config;
- }
-
- @JsonIgnore
- public String getFormat()
- {
- return format;
- }
-
- public void setFormat(String format)
- {
- this.format = format;
- }
-
- @JsonIgnore
- public String getBytes()
- {
- return bytes;
- }
-
- public void setBytes(String bytes)
- {
- this.bytes = bytes;
- }
-
- @JsonIgnore
- public boolean isShow()
- {
- return show;
- }
-
- public void setShow(boolean show)
- {
- this.show = show;
- }
-
- @JsonIgnore
- public Map<String, String> getMetaData()
- {
- return metaData;
- }
-
- public void setMetaData(Map<String, String> metaData)
- {
- this.metaData = metaData;
- }
-
- @Override
- public String toString()
- {
- return "ImagingDataSetPreview";
- }
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPropertyConfig.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPropertyConfig.java
deleted file mode 100644
index 7b9d9b71eb00bd109bb61218469ab131e72cc009..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPropertyConfig.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
-
-import ch.systemsx.cisd.base.annotation.JsonObject;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import java.io.Serializable;
-import java.util.List;
-
-@JsonObject("dss.dto.imaging.ImagingDataSetPropertyConfig")
-public class ImagingDataSetPropertyConfig implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- @JsonProperty
- ImagingDataSetConfig config;
-
- @JsonProperty
- List<ImagingDataSetImage> images;
-
- @JsonIgnore
- public ImagingDataSetConfig getConfig()
- {
- return config;
- }
-
- public void setConfig(ImagingDataSetConfig config)
- {
- this.config = config;
- }
-
- @JsonIgnore
- public List<ImagingDataSetImage> getImages()
- {
- return images;
- }
-
- public void setImages(
- List<ImagingDataSetImage> images)
- {
- this.images = images;
- }
-
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingArchiver.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingArchiver.java
deleted file mode 100644
index b550053a46c271b9bb670f8ee0bb503fb6df6f1d..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingArchiver.java
+++ /dev/null
@@ -1,157 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDataSetPackager;
-import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreServer;
-import ch.systemsx.cisd.openbis.dss.generic.server.TarDataSetPackager;
-import ch.systemsx.cisd.openbis.dss.generic.server.ZipDataSetPackager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.ISessionWorkspaceProvider;
-import org.apache.commons.io.FileUtils;
-
-import java.io.*;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.*;
-import java.util.function.Function;
-
-class ImagingArchiver
-{
- private final String sessionToken;
- private final String exportDirName;
- private final String exportArchiveName;
- private final Function<InputStream, Long> checksumFunction;
- private final AbstractDataSetPackager packager;
- private final File archiveFile;
- private boolean isFinished;
- private final long archiveDate;
-
- private static final int DEFAULT_BUFFER_SIZE = (int) (10 * FileUtils.ONE_MB);
-
- ImagingArchiver(String sessionToken, String archiveFormat) throws IOException {
- this.sessionToken = sessionToken;
- isFinished = false;
-
- archiveDate = System.currentTimeMillis();
- exportDirName = "imaging_export_" + String.valueOf(archiveDate);
-
- ISessionWorkspaceProvider sessionWorkspaceProvider = getSessionWorkspaceProvider(sessionToken);
- File rootDirectory = sessionWorkspaceProvider.getSessionWorkspace();
-
- Path tempDir = Files.createDirectory(
- Path.of(rootDirectory.getAbsolutePath(), exportDirName));
-
-
- if (archiveFormat.equalsIgnoreCase("zip"))
- {
- exportArchiveName = "export.zip";
- archiveFile =
- Files.createFile(Path.of(tempDir.toAbsolutePath().toString(), exportArchiveName))
- .toFile();
- packager = new ZipDataSetPackager(archiveFile, true, null, null);
- checksumFunction = Util::getCRC32Checksum;
- } else if (archiveFormat.equalsIgnoreCase("tar"))
- {
- exportArchiveName = "export.tar.gz";
- archiveFile =
- Files.createFile(Path.of(tempDir.toAbsolutePath().toString(), exportArchiveName))
- .toFile();
- packager = new TarDataSetPackager(archiveFile, null, null, DEFAULT_BUFFER_SIZE,
- 5L * DEFAULT_BUFFER_SIZE);
- checksumFunction = (x) -> 0L;
- } else
- {
- throw new UserFailureException("Unknown archive format!");
- }
-
-
- }
-
- void addToArchive(String folderName, String fileName, byte[] byteArray) {
- assertNotFinished();
- long size = byteArray.length;
- packager.addEntry(Paths.get(folderName, fileName).toString(),
- archiveDate,
- size,
- checksumFunction.apply(new ByteArrayInputStream(byteArray)),
- new ByteArrayInputStream(byteArray));
- }
-
- void addToArchive(String folderName, File fileOrDirectoryToArchive) {
- assertNotFinished();
-
- Deque<Map.Entry<String, File>> queue = new LinkedList<>();
-
- queue.add(new AbstractMap.SimpleImmutableEntry<>(folderName, fileOrDirectoryToArchive));
- while (!queue.isEmpty())
- {
- Map.Entry<String, File> element = queue.pollFirst();
- String prefixPath = element.getKey();
- File file = element.getValue();
- String path = Paths.get(prefixPath, file.getName()).toString();
- if (file.isDirectory())
- {
- for (File f : file.listFiles())
- {
- queue.add(new AbstractMap.SimpleImmutableEntry<>(path, f));
- }
- packager.addDirectoryEntry(path);
- } else
- {
- try
- {
- packager.addEntry(path,
- file.lastModified(),
- file.getTotalSpace(),
- checksumFunction.apply(new FileInputStream(file)),
- new FileInputStream(file));
- } catch (IOException exc)
- {
- throw new UserFailureException("Failed during export!", exc);
- }
- }
- }
-
- }
-
- String build() {
- if(!isFinished) {
- isFinished = true;
- packager.close();
- }
- String url = DataStoreServer.getConfigParameters().getDownloadURL() + "/datastore_server/session_workspace_file_download?sessionID=" + sessionToken + "&filePath=";
- return url + Path.of(exportDirName, exportArchiveName);
- }
-
- private ISessionWorkspaceProvider getSessionWorkspaceProvider(String sessionToken)
- {
- return ServiceProvider.getDataStoreService().getSessionWorkspaceProvider(sessionToken);
- }
-
- private void assertNotFinished()
- {
- if(isFinished){
- throw new UserFailureException("Archive file is already closed!");
- }
- }
-
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java
deleted file mode 100644
index 6c1278fddd9ba657e57e074b5ae51ce690ed9174..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java
+++ /dev/null
@@ -1,398 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetchOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
-import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetImage;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetMultiExport;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetPreview;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetPropertyConfig;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.CustomDSSServiceExecutionOptions;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.id.ICustomDSSServiceId;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.adaptor.IImagingDataSetAdaptor;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container.ImagingDataContainer;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container.ImagingExportContainer;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container.ImagingMultiExportContainer;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container.ImagingPreviewContainer;
-import ch.ethz.sis.openbis.generic.dssapi.v3.plugin.service.ICustomDSSServiceExecutor;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.reflection.ClassUtils;
-import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
-import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDataSetPackager;
-import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreServer;
-import ch.systemsx.cisd.openbis.dss.generic.server.TarDataSetPackager;
-import ch.systemsx.cisd.openbis.dss.generic.server.ZipDataSetPackager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.ISessionWorkspaceProvider;
-import ch.systemsx.cisd.openbis.generic.shared.dto.OpenBISSessionHolder;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-
-import java.io.*;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.*;
-import java.util.function.Function;
-
-public class ImagingService implements ICustomDSSServiceExecutor
-{
-
- private final Properties properties;
-
- private IHierarchicalContentProvider contentProvider;
-
- private static final Logger
- operationLog = LogFactory.getLogger(LogCategory.OPERATION, ImagingService.class);
-
- private static final int DEFAULT_BUFFER_SIZE = (int) (10 * FileUtils.ONE_MB);
-
- private static final String IMAGING_CONFIG_PROPERTY_NAME = "$IMAGING_DATA_CONFIG";
-
- public ImagingService(Properties properties)
- {
- this.properties = properties;
- }
-
- @Override
- public Serializable executeService(String sessionToken, ICustomDSSServiceId serviceId,
- CustomDSSServiceExecutionOptions options)
- {
- operationLog.info("Executing imaging service:" + serviceId);
- ImagingDataContainer data = getDataFromParams(options.getParameters());
- try
- {
- if (data.getType().equalsIgnoreCase("preview"))
- {
- return processPreviewFlow(sessionToken, (ImagingPreviewContainer) data);
- } else if (data.getType().equalsIgnoreCase("export"))
- {
- return processExportFlow(sessionToken, (ImagingExportContainer) data);
- } else if (data.getType().equalsIgnoreCase("multi-export"))
- {
- return processMultiExportFlow(sessionToken, (ImagingMultiExportContainer) data);
- } else
- {
- throw new UserFailureException("Unknown request type!");
- }
- } catch (Exception e)
- {
- data.setError(e.toString());
- }
- return data;
- }
-
- private IImagingDataSetAdaptor getAdaptor(ImagingDataSetPropertyConfig config)
- {
- final String adaptorName = config.getConfig().getAdaptor();
-
- if (adaptorName == null || adaptorName.isBlank())
- {
- throw new UserFailureException("Adaptor name is missing from the config!");
- }
- try
- {
- return ClassUtils.create(IImagingDataSetAdaptor.class, adaptorName, properties);
- } catch (Exception e)
- {
- throw new UserFailureException("Could not load adapter: " + adaptorName, e);
- }
- }
-
- private File getRootFile(String sessionToken, DataSet dataSet)
- {
- IHierarchicalContent content =
- getHierarchicalContentProvider(sessionToken).asContent(
- dataSet.getPermId().getPermId());
- IHierarchicalContentNode root = content.getRootNode();
- return root.getFile();
- }
-
- private ImagingPreviewContainer processPreviewFlow(String sessionToken,
- ImagingPreviewContainer data)
- {
- DataSet dataSet = getDataSet(sessionToken, data.getPermId());
-
- ImagingDataSetPropertyConfig config =
- Util.readConfig(dataSet.getJsonProperty("$IMAGING_DATA_CONFIG"),
- ImagingDataSetPropertyConfig.class);
-
- IImagingDataSetAdaptor adaptor = getAdaptor(config);
- File rootFile = getRootFile(sessionToken, dataSet);
- Map<String, Serializable> previewParams = data.getPreview().getConfig();
- Map<String, String> meta = data.getPreview().getMetaData();
- String format = data.getPreview().getFormat();
-
- int index = data.getIndex();
- if (config.getImages().size() <= index)
- {
- throw new UserFailureException("There is no image with index:" + index);
- }
- Map<String, Serializable> imageConfig = config.getImages().get(index).getConfig();
-
- if (format == null || format.isBlank())
- {
- throw new UserFailureException("Format can not be empty!");
- }
-
- ImagingServiceContext context =
- new ImagingServiceContext(sessionToken, getApplicationServerApi(),
- getDataStoreServerApi());
-
- data.getPreview().setBytes(
- adaptor.process(context,
- rootFile, imageConfig, previewParams, meta, format).toString());
- return data;
- }
-
-
-
- private Serializable processExportFlow(String sessionToken, ImagingExportContainer data)
- {
- // Get all parameters
- final DataSet dataSet = getDataSet(sessionToken, data.getPermId());
- final ImagingDataSetPropertyConfig config =
- Util.readConfig(dataSet.getJsonProperty(IMAGING_CONFIG_PROPERTY_NAME),
- ImagingDataSetPropertyConfig.class);
-
- final File rootFile = getRootFile(sessionToken, dataSet);
- final int index = data.getIndex();
- if (config.getImages().size() <= index)
- {
- throw new UserFailureException("There is no image with index:" + index);
- }
-
- final ImagingDataSetImage image = config.getImages().get(index);
-
- // TODO: discuss image config as filtering for export
- Map<String, Serializable> imageConfig = image.getConfig();
-
- Map<String, Serializable> exportConfig = data.getExport().getConfig();
- Validator.validateExportConfig(exportConfig);
-
- Serializable[] exportTypes = (Serializable[]) exportConfig.get("include");
-
- ImagingArchiver archiver;
-
- // Prepare archiver
- try
- {
- archiver = new ImagingArchiver(sessionToken, exportConfig.get("archive-format").toString());
- } catch (IOException exception)
- {
- throw new UserFailureException("Could not export data!", exception);
- }
-
- // For each export type, perform adequate action
- for (Serializable exportType : exportTypes)
- {
- if (exportType.toString().equalsIgnoreCase("image"))
- {
- ImagingServiceContext context =
- new ImagingServiceContext(sessionToken, getApplicationServerApi(),
- getDataStoreServerApi());
- IImagingDataSetAdaptor adaptor = getAdaptor(config);
- archiveImage(context, adaptor, image, index, exportConfig, rootFile, "", archiver);
- } else if (exportType.toString().equalsIgnoreCase("raw data"))
- {
- archiveRawData(rootFile, "", archiver, dataSet);
- } else
- {
- throw new UserFailureException("Unknown export type!");
- }
-
- }
-
- data.setUrl(archiver.build());
- return data;
- }
-
- private Serializable processMultiExportFlow(String sessionToken, ImagingMultiExportContainer data)
- {
- // multi export case
- final String archiveFormat = "zip";
- ImagingArchiver archiver;
- try
- {
- archiver = new ImagingArchiver(sessionToken, archiveFormat);
- } catch (IOException exception)
- {
- throw new UserFailureException("Could not export data!", exception);
- }
-
- for (ImagingDataSetMultiExport export : data.getExports())
- {
- DataSet dataSet = getDataSet(sessionToken, export.getPermId());
- ImagingDataSetPropertyConfig config =
- Util.readConfig(dataSet.getJsonProperty(IMAGING_CONFIG_PROPERTY_NAME),
- ImagingDataSetPropertyConfig.class);
-
- File rootFile = getRootFile(sessionToken, dataSet);
-
- final int index = export.getIndex();
- if (config.getImages().size() <= index)
- {
- throw new UserFailureException("There is no image with index:" + index);
- }
-
- ImagingDataSetImage image = config.getImages().get(index);
-
- // TODO: discuss image config as filtering for export
- Map<String, Serializable> imageConfig = image.getConfig();
-
- Map<String, Serializable> exportConfig = export.getConfig();
- Validator.validateExportConfig(exportConfig);
-
- Serializable[] exportTypes = (Serializable[]) exportConfig.get("include");
-
- // For each export type, perform adequate action
- for (Serializable exportType : exportTypes)
- {
- if (exportType.toString().equalsIgnoreCase("image"))
- {
- ImagingServiceContext context =
- new ImagingServiceContext(sessionToken, getApplicationServerApi(),
- getDataStoreServerApi());
- IImagingDataSetAdaptor adaptor = getAdaptor(config);
- archiveImage(context, adaptor, image, index, exportConfig, rootFile, export.getPermId(), archiver);
- } else if (exportType.toString().equalsIgnoreCase("raw data"))
- {
- archiveRawData(rootFile, export.getPermId(), archiver, dataSet);
- } else
- {
- throw new UserFailureException("Unknown export type!");
- }
-
- }
- }
- data.setUrl(archiver.build());
- return data;
- }
-
-
- private IHierarchicalContentProvider getHierarchicalContentProvider(String sessionToken)
- {
- if (contentProvider == null)
- {
- contentProvider = ServiceProvider.getHierarchicalContentProvider();
- }
- OpenBISSessionHolder sessionTokenHolder = new OpenBISSessionHolder();
- sessionTokenHolder.setSessionToken(sessionToken);
- return contentProvider.cloneFor(sessionTokenHolder);
- }
-
- private IApplicationServerApi getApplicationServerApi()
- {
- return ServiceProvider.getV3ApplicationService();
- }
-
- private IDataStoreServerApi getDataStoreServerApi()
- {
- return ServiceProvider.getV3DataStoreService();
- }
-
- private DataSet getDataSet(String sessionToken, String permId)
- {
- DataSetFetchOptions fetchOptions = new DataSetFetchOptions();
- fetchOptions.withProperties();
- fetchOptions.withType();
- fetchOptions.withDataStore();
- fetchOptions.withPhysicalData();
- Map<IDataSetId, DataSet> result = getApplicationServerApi()
- .getDataSets(sessionToken, List.of(new DataSetPermId(permId)),
- fetchOptions);
- if (result.isEmpty())
- {
- throw new UserFailureException("Could not find Dataset:" + permId);
- }
- return result.get(new DataSetPermId(permId));
- }
-
-
-
- private ImagingDataContainer getDataFromParams(Map<String, Object> params)
- {
- Validator.validateInputParams(params);
-
- String type = (String) params.get("type");
- String json = Util.mapToJson(params);
-
- switch (type.toLowerCase())
- {
- case "preview":
- return Util.readConfig(json, ImagingPreviewContainer.class);
- case "export":
- return Util.readConfig(json, ImagingExportContainer.class);
- case "multi-export":
- return Util.readConfig(json, ImagingMultiExportContainer.class);
- default:
- throw new UserFailureException("Wrong type:" + type);
- }
- }
-
- private void archiveRawData(File rootFile, String rootFolderName,
- ImagingArchiver archiver, DataSet dataSet)
- {
- //Add dataset files to archive
- archiver.addToArchive(rootFolderName, rootFile);
- //Add dataset properties to archive
- Map<String, Serializable> properties = dataSet.getProperties();
- properties.remove(IMAGING_CONFIG_PROPERTY_NAME);
- if(!properties.isEmpty()) {
- byte[] json = Util.mapToJson(properties).getBytes(StandardCharsets.UTF_8);
- archiver.addToArchive(rootFolderName, "properties.txt", json);
- }
- }
-
-
- private void archiveImage(ImagingServiceContext context, IImagingDataSetAdaptor adaptor,
- ImagingDataSetImage image, int imageIdx, Map<String, Serializable> exportConfig,
- File rootFile, String rootFolderName, ImagingArchiver archiver) {
-
- String imageFormat = exportConfig.get("image-format").toString();
- int previewIdx = 0;
- for(ImagingDataSetPreview preview : image.getPreviews())
- {
- String format = imageFormat;
- if(imageFormat.equalsIgnoreCase("original")) {
- format = preview.getFormat();
- }
- Map<String, Serializable> params = preview.getConfig();
- params.put("resolution", exportConfig.get("resolution"));
- Serializable img = adaptor.process(context,
- rootFile, image.getConfig(), params, image.getMetaData(), format);
- String imgString = img.toString();
- byte[] decoded = Base64.getDecoder().decode(imgString);
- String fileName = "image" + imageIdx +"_preview" + previewIdx + "." + format;
-
- archiver.addToArchive(rootFolderName, fileName, decoded);
- previewIdx++;
- }
- }
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingServiceContext.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingServiceContext.java
deleted file mode 100644
index b6d33d169f693b2627a59584c6e9219df75e63ef..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingServiceContext.java
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
-import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
-
-import java.io.Serializable;
-
-public final class ImagingServiceContext implements Serializable
-{
-
- private final String sessionToken;
- private final IApplicationServerApi asApi;
- private final IDataStoreServerApi dssApi;
-
-
- public ImagingServiceContext(String sessionToken, IApplicationServerApi asApi, IDataStoreServerApi dssApi) {
- this.sessionToken = sessionToken;
- this.asApi = asApi;
- this.dssApi = dssApi;
- }
-
- public String getSessionToken()
- {
- return sessionToken;
- }
-
- public IApplicationServerApi getAsApi()
- {
- return asApi;
- }
-
- public IDataStoreServerApi getDssApi()
- {
- return dssApi;
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Util.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Util.java
deleted file mode 100644
index f39f10af48cc54037c6bf6f1d10b37d4db0a1283..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Util.java
+++ /dev/null
@@ -1,137 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDataSetPackager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import com.fasterxml.jackson.databind.JsonMappingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import java.io.*;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Paths;
-import java.util.AbstractMap;
-import java.util.Deque;
-import java.util.LinkedList;
-import java.util.Map;
-import java.util.function.Function;
-import java.util.zip.CRC32;
-
-class Util
-{
- private Util() {}
-
- private static ObjectMapper getObjectMapper()
- {
- return ServiceProvider.getObjectMapperV3();
- }
-
- static long getCRC32Checksum(InputStream input)
- {
- if (input == null)
- throw new UserFailureException("Can not compute crc32!");
- CRC32 crc = new CRC32();
- byte[] buffer = new byte[4096];
- try
- {
- while (true)
- {
- int length = input.read(buffer);
- if (length == -1)
- break;
- crc.update(buffer, 0, length);
- }
- } catch (Exception ex)
- {
- try
- {
- input.close();
- } catch (Exception ignored)
- {
- }
- }
- return crc.getValue();
- }
-
- static <T> T readConfig(String val, Class<T> clazz)
- {
- try
- {
- ObjectMapper objectMapper = getObjectMapper();
- return objectMapper.readValue(new ByteArrayInputStream(val.getBytes()),
- clazz);
- } catch (JsonMappingException mappingException)
- {
- throw new UserFailureException(mappingException.toString(), mappingException);
- } catch (Exception e)
- {
- throw new UserFailureException("Could not read the parameters!", e);
- }
- }
-
- static String mapToJson(Map<String, ?> map)
- {
- try
- {
- ObjectMapper objectMapper = getObjectMapper();
- return objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
- } catch (Exception e)
- {
- throw new UserFailureException("Could not serialize the input parameters!", e);
- }
- }
-
-
-
- static void archiveFiles(AbstractDataSetPackager packager, File rootFile, String rootFolderName,
- Function<InputStream, Long> checksumFunction)
- {
- Deque<Map.Entry<String, File>> queue = new LinkedList<>();
-
- queue.add(new AbstractMap.SimpleImmutableEntry<>(rootFolderName, rootFile));
- while (!queue.isEmpty())
- {
- Map.Entry<String, File> element = queue.pollFirst();
- String prefixPath = element.getKey();
- File file = element.getValue();
- String path = Paths.get(prefixPath, file.getName()).toString();
- if (file.isDirectory())
- {
- for (File f : file.listFiles())
- {
- queue.add(new AbstractMap.SimpleImmutableEntry<>(path, f));
- }
- packager.addDirectoryEntry(path);
- } else
- {
- try
- {
- FileInputStream fileStream = new FileInputStream(file);
- packager.addEntry(path, file.lastModified(), file.getTotalSpace(),
- checksumFunction.apply(fileStream), new FileInputStream(file));
- } catch (IOException exc)
- {
- throw new UserFailureException("Failed during export!", exc);
- }
- }
- }
-
- }
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Validator.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Validator.java
deleted file mode 100644
index f9248caf9aac83c520671c849f7af9b3bbce2a1b..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Validator.java
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-import java.io.Serializable;
-import java.util.Map;
-
-class Validator
-{
- private Validator() {}
-
-
- static void validateInputParams(Map<String, Object> params)
- {
-// if (!params.containsKey("permId"))
-// {
-// throw new UserFailureException("Missing dataset permId!");
-// }
- if (!params.containsKey("type"))
- {
- throw new UserFailureException("Missing type!");
- }
-// if (!params.containsKey("index"))
-// {
-// throw new UserFailureException("Missing index!");
-// }
- }
-
-
- static void validateExportConfig(Map<String, Serializable> exportConfig) {
- if(exportConfig == null) {
- throw new UserFailureException("Export config can not be empty!");
- }
- validateTag(exportConfig, "include", true);
- validateTag(exportConfig, "image-format");
- validateTag(exportConfig, "archive-format");
- validateTag(exportConfig, "resolution");
- }
-
- private static void validateTag(Map<String, Serializable> config, String tagName)
- {
- validateTag(config, tagName, false);
- }
-
- private static void validateTag(Map<String, Serializable> config, String tagName, boolean isMultiValue)
- {
- if(!config.containsKey(tagName)){
- throw new UserFailureException("Missing '"+tagName+"' in export config!");
- }
- Serializable include = config.get(tagName);
- if(include == null){
- throw new UserFailureException("'"+tagName+"' tag in export config can not be null!");
- }
- if(isMultiValue)
- {
- if (!include.getClass().isArray())
- {
- throw new UserFailureException("'include' tag in export config must be an array!");
- }
- if (((Serializable[]) include).length == 0)
- {
- throw new UserFailureException("'include' tag in export config can not be empty!");
- }
- }
- }
-
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java
deleted file mode 100644
index 536f083757128825e389b0966cf809fcc6c77305..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.adaptor;
-
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.ImagingServiceContext;
-
-import javax.imageio.ImageIO;
-import java.awt.image.BufferedImage;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.Serializable;
-import java.util.Base64;
-import java.util.Map;
-import java.util.Properties;
-
-public final class ImagingDataSetExampleAdaptor implements IImagingDataSetAdaptor
-{
-
- private static final int WIDTH = 640;
- private static final int HEIGHT = 640;
-
- public ImagingDataSetExampleAdaptor(Properties properties) {
- }
-
- @Override
- public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
- Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
- {
- BufferedImage img = new BufferedImage(WIDTH, HEIGHT, BufferedImage.TYPE_INT_ARGB);
- for(int y=0;y<HEIGHT; y++)
- {
- for (int x = 0; x < WIDTH; x++)
- {
- int a = (int)(Math.random()*256);
- int r = (int)(Math.random()*256);
- int g = (int)(Math.random()*256);
- int b = (int)(Math.random()*256);
-
- //pixel
- int p = (a<<24) | (r<<16) | (g<<8) | b;
-
- img.setRGB(x, y, p);
- }
- }
- try
- {
- ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
- ImageIO.write(img, "png", byteArrayOutputStream);
- byteArrayOutputStream.flush();
- return Base64.getEncoder().encodeToString(byteArrayOutputStream.toByteArray());
- } catch (Exception e) {
- throw new RuntimeException(e);
- }
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java
deleted file mode 100644
index 1a53bcd5c649ef0262d5cb142e1321b7556f82ef..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.adaptor;
-
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.CustomDSSServiceExecutionOptions;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.ImagingServiceContext;
-import ch.ethz.sis.openbis.generic.server.dssapi.v3.helper.IDssServiceScriptRunner;
-import ch.ethz.sis.openbis.generic.server.dssapi.v3.helper.ScriptRunnerFactory;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-import java.io.File;
-import java.io.Serializable;
-import java.util.Map;
-import java.util.Properties;
-
-public class ImagingDataSetJythonAdaptor implements IImagingDataSetAdaptor
-{
- private final String scriptPath;
-
-
- public ImagingDataSetJythonAdaptor(Properties properties) {
- this.scriptPath = properties.getProperty("script-path", "");
- if(scriptPath.isBlank()) {
- throw new UserFailureException("There is no script defined for this adaptor!");
- }
- }
- @Override
- public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
- Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
- {
- CustomDSSServiceExecutionOptions options = new CustomDSSServiceExecutionOptions();
- options.withParameter("sessionToken", context.getSessionToken());
- options.withParameter("asApi", context.getAsApi());
- options.withParameter("dssApi", context.getDssApi());
- options.withParameter("file", rootFile);
- options.withParameter("imageConfig", imageConfig);
- options.withParameter("config", previewConfig);
- options.withParameter("metaData", metaData);
- IDssServiceScriptRunner
- runner = new ScriptRunnerFactory(scriptPath, context.getAsApi(),
- context.getDssApi())
- .createServiceRunner(context.getSessionToken());
- return runner.process(options);
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java
deleted file mode 100644
index b616666b257ee6a3cae28f082b33c1f052cf1be6..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.adaptor;
-
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.ImagingServiceContext;
-import ch.ethz.sis.openbis.generic.server.sharedapi.v3.json.GenericObjectMapper;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.Serializable;
-import java.nio.charset.StandardCharsets;
-import java.util.HashMap;
-import java.util.Map;
-
-public abstract class ImagingDataSetPythonAdaptor implements IImagingDataSetAdaptor
-{
-
- protected String pythonPath;
-
- protected String scriptPath;
-
- @Override
- public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
- Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
- {
-
- ProcessBuilder processBuilder = new ProcessBuilder(pythonPath,
- scriptPath, rootFile.getAbsolutePath(), convertMapToJson(imageConfig),
- convertMapToJson(previewConfig), convertMapToJson(metaData), format);
- processBuilder.redirectErrorStream(false);
-
- String fullOutput;
- try
- {
- Process process = processBuilder.start();
- fullOutput =
- new String(process.getInputStream().readAllBytes(), StandardCharsets.UTF_8);
- int exitCode = process.waitFor();
- if (exitCode != 0)
- {
- String error =
- new String(process.getErrorStream().readAllBytes(), StandardCharsets.UTF_8);
- throw new UserFailureException("Script evaluation failed: " + error);
- }
- } catch (IOException | InterruptedException e)
- {
- throw new RuntimeException(e);
- }
-
- if (fullOutput.isBlank())
- {
- throw new UserFailureException("Script produced no results!");
- }
-
- String[] resultSplit = fullOutput.split("\n");
- return resultSplit[resultSplit.length - 1];
- }
-
- private String convertMapToJson(Map<String, ?> map)
- {
- Map<String, ?> mapToConvert = map;
- if(map == null) {
- mapToConvert = new HashMap<>();
- }
- try
- {
- ObjectMapper objectMapper = new GenericObjectMapper();
- return objectMapper.writeValueAsString(mapToConvert);
- } catch (Exception e)
- {
- throw new UserFailureException("Couldn't convert map to string", e);
- }
- }
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisDatAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisDatAdaptor.java
deleted file mode 100644
index 4b66f8cf576f1211667c0de0f8c9d48459a3e30c..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisDatAdaptor.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.adaptor;
-
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.ImagingServiceContext;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
-import java.io.File;
-import java.io.Serializable;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.Map;
-import java.util.Properties;
-
-public class NanonisDatAdaptor extends ImagingDataSetPythonAdaptor
-{
- private final String DAT_SCRIPT_PROPERTY = "nanonis-dat";
-
-
- public NanonisDatAdaptor(Properties properties)
- {
-
- String scriptProperty = properties.getProperty(DAT_SCRIPT_PROPERTY, "");
- if (scriptProperty.isBlank())
- {
- throw new UserFailureException(
- "There is no script path property called '" + DAT_SCRIPT_PROPERTY + "' defined for this adaptor!");
- }
- Path script = Paths.get(scriptProperty);
- if (!Files.exists(script))
- {
- throw new UserFailureException("Script file " + script + " does not exists!");
- }
- this.scriptPath = script.toString();
- this.pythonPath = properties.getProperty("python3-path", "python3");
- }
-
- @Override
- public Serializable process(
- ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
- Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
- {
- Serializable result = super.process(context, rootFile, imageConfig, previewConfig, metaData, format);
- if (result == null)
- {
- return result;
- }
- String str = result.toString();
- if (str.length() > 3)
- {
- return str.substring(2, str.length() - 1);
- } else
- {
- return "";
- }
-
- }
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisSxmAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisSxmAdaptor.java
deleted file mode 100644
index 4f7601ec881634e0f4cb15aea41424c6d4f6e023..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisSxmAdaptor.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.adaptor;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.ImagingServiceContext;
-import ch.ethz.sis.openbis.generic.server.sharedapi.v3.json.GenericObjectMapper;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.Serializable;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.Map;
-import java.util.Properties;
-
-public final class NanonisSxmAdaptor extends ImagingDataSetPythonAdaptor
-{
- private final String SXM_SCRIPT_PROPERTY = "nanonis-sxm";
-
- public NanonisSxmAdaptor(Properties properties)
- {
-
- String scriptProperty = properties.getProperty(SXM_SCRIPT_PROPERTY, "");
- if (scriptProperty.isBlank())
- {
- throw new UserFailureException(
- "There is no script path property called '" + SXM_SCRIPT_PROPERTY + "' defined for this adaptor!");
- }
- Path script = Paths.get(scriptProperty);
- if (!Files.exists(script))
- {
- throw new UserFailureException("Script file " + script + " does not exists!");
- }
- this.scriptPath = script.toString();
- this.pythonPath = properties.getProperty("python3-path", "python3");
- }
-
- @Override
- public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
- Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
- {
- Serializable result = super.process(context, rootFile, imageConfig, previewConfig, metaData, format);
- if (result == null)
- {
- return result;
- }
- String str = result.toString();
- if (str.length() > 3)
- {
- return str.substring(2, str.length() - 1);
- } else
- {
- return "";
- }
-
- }
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingDataContainer.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingDataContainer.java
deleted file mode 100644
index 7c07d1c0b91e069e1ef724080a415d42e9d85731..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingDataContainer.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import java.io.Serializable;
-
-public abstract class ImagingDataContainer implements Serializable
-{
-
- @JsonProperty
- private String type;
-
- @JsonProperty
- private String error;
-
- @JsonIgnore
- public String getType()
- {
- return type;
- }
-
- public void setType(String type) {
- this.type = type;
- }
-
- @JsonIgnore
- public String getError()
- {
- return error;
- }
-
- public void setError(String error)
- {
- this.error = error;
- }
-
-
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingExportContainer.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingExportContainer.java
deleted file mode 100644
index c1e5fed445dd53bd0180b554737cffabddf1e5eb..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingExportContainer.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container;
-
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetExport;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public final class ImagingExportContainer extends ImagingDataContainer
-{
-
- @JsonProperty
- private String permId;
- @JsonProperty
- private int index;
- @JsonProperty
- private String url;
- @JsonProperty
- private ImagingDataSetExport export = null;
-
- @JsonIgnore
- public String getPermId()
- {
- return permId;
- }
-
- public void setPermId(String permId) {
- this.permId = permId;
- }
-
- @JsonIgnore
- public int getIndex()
- {
- return index;
- }
-
- public void setIndex(int index) {
- this.index = index;
- }
-
- @JsonIgnore
- public String getUrl()
- {
- return url;
- }
-
- public void setUrl(String url)
- {
- this.url = url;
- }
-
- @JsonIgnore
- public ImagingDataSetExport getExport()
- {
- return export;
- }
-
- public void setExport(ImagingDataSetExport export)
- {
- this.export = export;
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingMultiExportContainer.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingMultiExportContainer.java
deleted file mode 100644
index 183cb54dfd5fb69afa6cd336000f53d1713dc9e7..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingMultiExportContainer.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container;
-
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetMultiExport;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-import java.util.List;
-
-public class ImagingMultiExportContainer extends ImagingDataContainer
-{
-
- @JsonProperty
- private String url;
-
- @JsonProperty
- private List<ImagingDataSetMultiExport> exports = null;
-
- @JsonIgnore
- public String getUrl()
- {
- return url;
- }
-
- public void setUrl(String url)
- {
- this.url = url;
- }
-
- @JsonIgnore
- public List<ImagingDataSetMultiExport> getExports()
- {
- return exports;
- }
-
- public void setExports(List<ImagingDataSetMultiExport> exports)
- {
- this.exports = exports;
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingPreviewContainer.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingPreviewContainer.java
deleted file mode 100644
index d5d5e23973d6b1a1c328a3a11c96cef27e0687bc..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingPreviewContainer.java
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container;
-
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetPreview;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-
-public final class ImagingPreviewContainer extends ImagingDataContainer
-{
-
- @JsonProperty
- private String permId;
- @JsonProperty
- private int index;
- @JsonProperty
- private ImagingDataSetPreview preview = null;
-
- @JsonIgnore
- public String getPermId()
- {
- return permId;
- }
-
- public void setPermId(String permId) {
- this.permId = permId;
- }
-
- @JsonIgnore
- public int getIndex()
- {
- return index;
- }
-
- public void setIndex(int index) {
- this.index = index;
- }
-
- @JsonIgnore
- public ImagingDataSetPreview getPreview()
- {
- return preview;
- }
-
- public void setPreview(ImagingDataSetPreview preview)
- {
- this.preview = preview;
- }
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetConfig.js b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetConfig.js
deleted file mode 100644
index c44fe0fac0f436f2cfd003518eb036709e0e4e08..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetConfig.js
+++ /dev/null
@@ -1,91 +0,0 @@
-define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
- var ImagingDataSetConfig = function() {
- };
- stjs.extend(ImagingDataSetConfig, null, [], function(constructor, prototype) {
- prototype['@type'] = 'dss.dto.imaging.ImagingDataSetConfig';
- constructor.serialVersionUID = 1;
- prototype.adaptor = null;
- prototype.version = null;
- prototype.speeds = null;
- prototype.resolutions = null;
- prototype.playable = null;
- prototype.exports = null;
- prototype.inputs = null;
- prototype.metaData = null;
-
- prototype.getAdaptor = function() {
- return this.adaptor;
- };
- prototype.setAdaptor = function(adaptor) {
- this.adaptor = adaptor;
- };
- prototype.getVersion = function() {
- return this.version;
- };
- prototype.setVersion = function(version) {
- this.version = version;
- };
- prototype.getSpeeds = function() {
- return this.speeds;
- };
- prototype.setSpeeds = function(speeds) {
- this.speeds = speeds;
- };
- prototype.getResolutions = function() {
- return this.resolutions;
- };
- prototype.setResolutions = function(resolutions) {
- this.resolutions = resolutions;
- };
- prototype.getPlayable = function() {
- return this.playable;
- };
- prototype.setPlayable = function(playable) {
- this.playable = playable;
- };
- prototype.getExports = function() {
- return this.exports;
- };
- prototype.setExports = function(exports) {
- this.exports = exports;
- };
- prototype.getInputs = function() {
- return this.inputs;
- };
- prototype.setInputs = function(inputs) {
- this.inputs = inputs;
- };
- prototype.getMetaData = function() {
- return this.metaData;
- };
- prototype.setMetaData = function(metaData) {
- this.metaData = metaData;
- };
- prototype.toString = function() {
- return "ImagingDataSetConfig: " + this.adaptor;
- };
-
- }, {
- resolutions : {
- name : "List",
- arguments : [ "String"]
- },
- speeds : {
- name : "List",
- arguments : [ "Integer"]
- },
- exports : {
- name : "List",
- arguments : [ "ImagingDataSetControl"]
- },
- inputs : {
- name : "List",
- arguments : [ "ImagingDataSetControl"]
- },
- metaData : {
- name : "Map",
- arguments : [ "String", "String" ]
- }
- });
- return ImagingDataSetConfig;
-})
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetControl.js b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetControl.js
deleted file mode 100644
index 30c9b6c9a3839bec4abcb37efcb50d2bb12f6e2b..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetControl.js
+++ /dev/null
@@ -1,112 +0,0 @@
-define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
- var ImagingDataSetControl = function() {
- };
- stjs.extend(ImagingDataSetControl, null, [], function(constructor, prototype) {
- prototype['@type'] = 'dss.dto.imaging.ImagingDataSetControl';
- constructor.serialVersionUID = 1;
- prototype.label = null;
- prototype.section = null;
- prototype.type = null;
- prototype.values = null;
- prototype.unit = null;
- prototype.range = null;
- prototype.multiselect = null;
- prototype.playable = null;
- prototype.speeds = null;
- prototype.visibility = null;
- prototype.metaData = null;
-
- prototype.getLabel = function() {
- return this.label;
- };
- prototype.setLabel = function(label) {
- this.label = label;
- };
- prototype.getSection = function() {
- return this.section;
- };
- prototype.setSection = function(section) {
- this.section = section;
- };
- prototype.getType = function() {
- return this.type;
- };
- prototype.setType = function(type) {
- this.type = type;
- };
- prototype.getValues = function() {
- return this.values;
- };
- prototype.setValues = function(values) {
- this.values = values;
- };
- prototype.getUnit = function() {
- return this.unit;
- };
- prototype.setUnit = function(unit) {
- this.unit = unit;
- };
- prototype.getRange = function() {
- return this.range;
- };
- prototype.setRange = function(range) {
- this.range = range;
- };
- prototype.getMultiselect = function() {
- return this.multiselect;
- };
- prototype.setMultiselect = function(multiselect) {
- this.multiselect = multiselect;
- };
- prototype.getPlayable = function() {
- return this.playable;
- };
- prototype.setPlayable = function(playable) {
- this.playable = playable;
- };
- prototype.getSpeeds = function() {
- return this.speeds;
- };
- prototype.setSpeeds = function(speeds) {
- this.speeds = speeds;
- };
- prototype.getVisibility = function() {
- return this.visibility;
- };
- prototype.setVisibility = function(visibility) {
- this.visibility = visibility;
- };
- prototype.getMetaData = function() {
- return this.metaData;
- };
- prototype.setMetaData = function(metaData) {
- this.metaData = metaData;
- };
- prototype.toString = function() {
- return "ImagingDataSetControl: " + this.label;
- };
-
- }, {
- values : {
- name : "List",
- arguments : [ "String"]
- },
- visibility: {
- name : "List",
- arguments : [ "ImagingDataSetControlVisibility"]
- }
- range : {
- name : "List",
- arguments : [ "String"]
- },
- speeds : {
- name : "List",
- arguments : [ "Integer"]
- },
- metaData : {
- name : "Map",
- arguments : [ "String", "String" ]
- }
- });
- return ImagingDataSetControl;
-})
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetControlVisibility.js b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetControlVisibility.js
deleted file mode 100644
index 5a0b2fc77113238ba19ca6f3f2caa8b2df23e1e2..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetControlVisibility.js
+++ /dev/null
@@ -1,51 +0,0 @@
-define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
- var ImagingDataSetControlVisibility = function() {
- };
- stjs.extend(ImagingDataSetControlVisibility, null, [], function(constructor, prototype) {
- prototype['@type'] = 'dss.dto.imaging.ImagingDataSetControlVisibility';
- constructor.serialVersionUID = 1;
- prototype.label = null;
- prototype.values = null;
- prototype.range = null;
- prototype.unit = null;
-
- prototype.getLabel = function() {
- return this.label;
- };
- prototype.setLabel = function(label) {
- this.label = label;
- };
- prototype.getValues = function() {
- return this.values;
- };
- prototype.setValues = function(values) {
- this.values = values;
- };
- prototype.getUnit = function() {
- return this.unit;
- };
- prototype.setUnit = function(unit) {
- this.unit = unit;
- };
- prototype.getRange = function() {
- return this.range;
- };
- prototype.setRange = function(range) {
- this.range = range;
- };
- prototype.toString = function() {
- return "ImagingDataSetControlVisibility: " + this.label;
- };
-
- }, {
- values : {
- name : "List",
- arguments : [ "String"]
- },
- range : {
- name : "List",
- arguments : [ "String"]
- }
- });
- return ImagingDataSetControlVisibility;
-})
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetExport.js b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetExport.js
deleted file mode 100644
index a478e50fcc69dc9aa59d2fa96e4fb2cfb15223a2..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetExport.js
+++ /dev/null
@@ -1,58 +0,0 @@
-define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
- var ImagingDataSetExport = function() {
- };
- stjs.extend(ImagingDataSetExport, null, [], function(constructor, prototype) {
- prototype['@type'] = 'dss.dto.imaging.ImagingDataSetExport';
- constructor.serialVersionUID = 1;
- prototype.config = null;
- prototype.format = null;
- prototype.bytes = null;
- prototype.show = null;
- prototype.metaData = null;
-
- prototype.getConfig = function() {
- return this.config;
- };
- prototype.setConfig = function(config) {
- this.config = config;
- };
- prototype.getFormat = function() {
- return this.format;
- };
- prototype.setFormat = function(format) {
- this.format = format;
- };
- prototype.getBytes = function() {
- return this.bytes;
- };
- prototype.setBytes = function(bytes) {
- this.bytes = bytes;
- };
- prototype.isShow = function() {
- return this.show;
- };
- prototype.setShow = function(show) {
- this.show = show;
- };
- prototype.getMetaData = function() {
- return this.metaData;
- };
- prototype.setMetaData = function(metaData) {
- this.metaData = metaData;
- };
- prototype.toString = function() {
- return "ImagingDataSetExport: " + this.config;
- };
-
- }, {
- config : {
- name : "Map",
- arguments : [ "String", "Serializable" ]
- },
- metaData : {
- name : "Map",
- arguments : [ "String", "String" ]
- }
- });
- return ImagingDataSetExport;
-})
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetImage.js b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetImage.js
deleted file mode 100644
index cabcef4beca86e165149c8398864e4d340ce3826..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetImage.js
+++ /dev/null
@@ -1,37 +0,0 @@
-define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
- var ImagingDataSetImage = function() {
- };
- stjs.extend(ImagingDataSetImage, null, [], function(constructor, prototype) {
- prototype['@type'] = 'dss.dto.imaging.ImagingDataSetImage';
- constructor.serialVersionUID = 1;
- prototype.previews = null;
- prototype.metaData = null;
-
- prototype.getPreviews = function() {
- return this.previews;
- };
- prototype.setPreviews = function(previews) {
- this.previews = previews;
- };
- prototype.getMetaData = function() {
- return this.metaData;
- };
- prototype.setMetaData = function(metaData) {
- this.metaData = metaData;
- };
- prototype.toString = function() {
- return "ImagingDataSetImage: " + this.previews;
- };
-
- }, {
- previews : {
- name : "List",
- arguments : [ "ImagingDataSetPreview"]
- },
- metaData : {
- name : "Map",
- arguments : [ "String", "String" ]
- }
- });
- return ImagingDataSetImage;
-})
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetPreview.js b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetPreview.js
deleted file mode 100644
index f119f0c2e32c9bad12c60203539ccf0e11fc55db..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetPreview.js
+++ /dev/null
@@ -1,58 +0,0 @@
-define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
- var ImagingDataSetPreview = function() {
- };
- stjs.extend(ImagingDataSetPreview, null, [], function(constructor, prototype) {
- prototype['@type'] = 'dss.dto.imaging.ImagingDataSetPreview';
- constructor.serialVersionUID = 1;
- prototype.config = null;
- prototype.format = null;
- prototype.bytes = null;
- prototype.show = null;
- prototype.metaData = null;
-
- prototype.getConfig = function() {
- return this.config;
- };
- prototype.setConfig = function(config) {
- this.config = config;
- };
- prototype.getFormat = function() {
- return this.format;
- };
- prototype.setFormat = function(format) {
- this.format = format;
- };
- prototype.getBytes = function() {
- return this.bytes;
- };
- prototype.setBytes = function(bytes) {
- this.bytes = bytes;
- };
- prototype.isShow = function() {
- return this.show;
- };
- prototype.setShow = function(show) {
- this.show = show;
- };
- prototype.getMetaData = function() {
- return this.metaData;
- };
- prototype.setMetaData = function(metaData) {
- this.metaData = metaData;
- };
- prototype.toString = function() {
- return "ImagingDataSetPreview: " + this.config;
- };
-
- }, {
- config : {
- name : "Map",
- arguments : [ "String", "Serializable" ]
- },
- metaData : {
- name : "Map",
- arguments : [ "String", "String" ]
- }
- });
- return ImagingDataSetPreview;
-})
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetPropertyConfig.js b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetPropertyConfig.js
deleted file mode 100644
index 3b0b820e8cc22a18c592b16ebab2c80c187eea92..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/js/src/v3/dss/dto/imaging/ImagingDataSetPropertyConfig.js
+++ /dev/null
@@ -1,34 +0,0 @@
-define([ "stjs", "util/Exceptions" ], function(stjs, exceptions) {
- var ImagingDataSetPropertyConfig = function() {
- };
- stjs.extend(ImagingDataSetPropertyConfig, null, [], function(constructor, prototype) {
- prototype['@type'] = 'dss.dto.imaging.ImagingDataSetPropertyConfig';
- constructor.serialVersionUID = 1;
- prototype.config = null;
- prototype.images = null;
-
- prototype.getConfig = function() {
- return this.config;
- };
- prototype.setConfig = function(config) {
- this.config = config;
- };
- prototype.getImages = function() {
- return this.images;
- };
- prototype.setSection = function(images) {
- this.images = images;
- };
-
- prototype.toString = function() {
- return "ImagingDataSetPropertyConfig: " + this.label;
- };
-
- }, {
- images : {
- name : "List",
- arguments : [ "ImagingDataSetImage"]
- }
- });
- return ImagingDataSetPropertyConfig;
-})
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/python/imaging/__init__.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/python/imaging/__init__.py
deleted file mode 100644
index ea4523e5b122686bfa54ed93a661088b4a834a54..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/python/imaging/__init__.py
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright ETH 2023 Zürich, Scientific IT Services
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-from . import imaging
-
-name = "imaging"
-__author__ = "ID SIS • ETH Zürich"
-__email__ = "openbis-support@id.ethz.ch"
-__version__ = "0.0.0"
-
-
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/python/imaging/imaging.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/python/imaging/imaging.py
deleted file mode 100644
index fccc9d84387642b648ebfef379d1d824b80fe9ed..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/python/imaging/imaging.py
+++ /dev/null
@@ -1,448 +0,0 @@
-# Copyright ETH 2023 Zürich, Scientific IT Services
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-from pybis import Openbis
-import abc
-import json
-import base64
-import requests
-import os
-from urllib.parse import urljoin
-
-
-DEFAULT_SERVICE_NAME = "imaging"
-IMAGING_CONFIG_PROP_NAME = "$IMAGING_DATA_CONFIG".lower()
-
-
-def get_instance(url="http://localhost:8888/openbis"):
- base_url = url
- # base_url = "http://localhost:8888/openbis"
- # base_url = "https://alaskowski:8443/openbis"
- # base_url = "https://openbis-sis-ci-sprint.ethz.ch/"
- openbis_instance = Openbis(
- url=base_url,
- verify_certificates=False,
- allow_http_but_do_not_use_this_in_production_and_only_within_safe_networks=True
- )
- token = openbis_instance.login('admin', 'changeit')
- print(f'Connected to {base_url} -> token: {token}')
- return openbis_instance
-
-
-class AbstractImagingClass(metaclass=abc.ABCMeta):
- def to_json(self):
- return json.dumps(self, default=lambda x: x.__dict__, sort_keys=True, indent=4)
-
- def __str__(self):
- return json.dumps(self.__dict__, default=lambda x: x.__dict__)
-
- def __repr__(self):
- return json.dumps(self.__dict__, default=lambda x: x.__dict__)
-
-
-class AbstractImagingRequest(AbstractImagingClass, metaclass=abc.ABCMeta):
- @abc.abstractmethod
- def _validate_data(self):
- return
-
-
-class ImagingDataSetPreview(AbstractImagingRequest):
- config: dict
- format: str
- bytes: str | None
- show: bool
- metadata: dict
-
- def __init__(self, config, preview_format, metadata=None):
- self.__dict__["@type"] = "dss.dto.imaging.ImagingDataSetPreview"
- self.bytes = None
- self.format = preview_format
- self.config = config if config is not None else dict()
- self.metadata = metadata if metadata is not None else dict()
- self._validate_data()
-
- def _validate_data(self):
- assert self.format is not None, "Format can not be null"
-
- def save_to_file(self, file_path):
- assert self.bytes is not None, "There is no image information!"
- img_data = bytearray(self.bytes, encoding='utf-8')
- with open(file_path, "wb") as fh:
- fh.write(base64.decodebytes(img_data))
-
- @classmethod
- def from_dict(cls, data):
- if data is None:
- return None
- preview = cls(None, None, None)
- for prop in cls.__annotations__.keys():
- attribute = data.get(prop)
- preview.__dict__[prop] = attribute
- return preview
-
-
-class ImagingDataSetExport(AbstractImagingRequest):
- config: dict
- metadata: dict
-
- def __init__(self, config, metadata=None):
- self.__dict__["@type"] = "dss.dto.imaging.ImagingDataSetExport"
- self.config = config if config is not None else dict()
- self.metadata = metadata if metadata is not None else dict()
- self._validate_data()
-
- def _validate_data(self):
- assert self.config is not None, "Config can not be null"
- required_keys = {"include", "archive-format", "image-format", "resolution"}
- for key in required_keys:
- assert key in self.config and self.config[key] is not None, \
- f"export->config->{key}: Must not be None!"
-
-
-class ImagingDataSetMultiExport(AbstractImagingRequest):
- permId: str
- index: int
- config: dict
- metadata: dict
-
- def __init__(self, permId, index, config, metadata=None):
- self.__dict__["@type"] = "dss.dto.imaging.ImagingDataSetMultiExport"
- self.permId = permId
- self.index = index
- self.config = config
- self.metadata = metadata if metadata is not None else dict()
- self._validate_data()
-
- def _validate_data(self):
- assert self.permId is not None, "PermId can not be null"
- assert self.index is not None, "Index can not be null"
- assert self.config is not None, "Config can not be null"
- required_keys = {"include", "archive-format", "image-format", "resolution"}
- for key in required_keys:
- assert key in self.config and self.config[key] is not None, \
- f"export->config->{key}: Must not be None!"
-
-
-class ImagingDataSetControlVisibility(AbstractImagingClass):
- label: str
- values: list[str]
- range: list[str]
- unit: str
-
- def __init__(self, label: str, values: list[str], values_range: list[str], unit: str = None):
- self.__dict__["@type"] = "dss.dto.imaging.ImagingDataSetControlVisibility"
- self.label = label
- self.values = values
- self.range = values_range
- self.unit = unit
-
- @classmethod
- def from_dict(cls, data):
- if data is None:
- return None
- control = cls(None, None, None, None)
- for prop in cls.__annotations__.keys():
- attribute = data.get(prop)
- control.__dict__[prop] = attribute
- return control
-
-
-class ImagingDataSetControl(AbstractImagingClass):
- label: str
- section: str
- type: str
- values: list[str]
- unit: str
- range: list[str]
- multiselect: bool
- playable: bool
- speeds: list[int]
- visibility: list[ImagingDataSetControlVisibility]
- metaData: dict
-
- def __init__(self, label: str, control_type: str, values: list[str] = None,
- values_range: list[str] = None, multiselect: bool = None):
- self.__dict__["@type"] = "dss.dto.imaging.ImagingDataSetControl"
- self.label = label
- self.type = control_type
- if control_type.lower() in ["slider", "range"]:
- self.range = values_range
- elif control_type.lower() == "dropdown":
- self.values = values
- self.multiselect = multiselect
-
- @classmethod
- def from_dict(cls, data):
- if data is None:
- return None
- control = cls(None, "", None, None)
- for prop in cls.__annotations__.keys():
- attribute = data.get(prop)
- if prop == 'visibility' and attribute is not None:
- attribute = [ImagingDataSetControlVisibility.from_dict(visibility) for visibility in attribute]
- control.__dict__[prop] = attribute
- return control
-
-
-class ImagingDataSetConfig(AbstractImagingClass):
- adaptor: str
- version: float
- speeds: list[int]
- resolutions: list[str]
- playable: bool
- exports: list[ImagingDataSetControl]
- inputs: list[ImagingDataSetControl]
- metadata: dict
-
- def __init__(self, adaptor: str, version: float, resolutions: list[str], playable: bool,
- speeds: list[int] = None, exports: list[ImagingDataSetControl] = None,
- inputs: list[ImagingDataSetControl] = None, metadata: dict = None):
- self.__dict__["@type"] = "dss.dto.imaging.ImagingDataSetConfig"
- self.adaptor = adaptor
- self.version = version
- self.resolutions = resolutions
- self.playable = playable
- if playable:
- self.speeds = speeds
- self.exports = exports
- self.inputs = inputs
- self.metadata = metadata
-
- @classmethod
- def from_dict(cls, data):
- if data is None:
- return None
- config = cls(None, None, None, None)
- for prop in cls.__annotations__.keys():
- attribute = data.get(prop)
- if prop in ['exports', 'inputs'] and attribute is not None:
- attribute = [ImagingDataSetControl.from_dict(control) for control in attribute]
- config.__dict__[prop] = attribute
- return config
-
-
-class ImagingDataSetImage(AbstractImagingClass):
- previews: list[ImagingDataSetPreview]
- config: dict
- metadata: dict
-
- def __init__(self, config=None, previews=None, metadata=None):
- self.__dict__["@type"] = "dss.dto.imaging.ImagingDataSetImage"
- self.config = config if config is not None else dict()
- self.previews = previews if previews is not None else []
- self.metadata = metadata if metadata is not None else dict()
-
- def add_preview(self, preview):
- self.previews += [preview]
-
- @classmethod
- def from_dict(cls, data):
- if data is None:
- return None
- image = cls(None, None, None)
- for prop in cls.__annotations__.keys():
- attribute = data.get(prop)
- if prop == 'images' and attribute is not None:
- attribute = [ImagingDataSetPreview.from_dict(image) for image in attribute]
- image.__dict__[prop] = attribute
- return image
-
-
-class ImagingDataSetPropertyConfig(AbstractImagingClass):
- config: ImagingDataSetConfig
- images: list[ImagingDataSetImage]
-
- def __init__(self, config: ImagingDataSetConfig, images: list[ImagingDataSetImage]):
- assert config is not None, "Config must not be None!"
- self.__dict__["@type"] = "dss.dto.imaging.ImagingDataSetPropertyConfig"
- self.config = config
- self.images = images if images is not None else []
-
- @classmethod
- def from_dict(cls, data: dict):
- assert data is not None and any(data), "There is no property config found!"
- config = ImagingDataSetConfig.from_dict(data.get('config'))
- attr = data.get('images')
- images = [ImagingDataSetImage.from_dict(image) for image in attr] if attr is not None else None
- return cls(config, images)
-
- def add_image(self, image: ImagingDataSetImage):
- if self.images is None:
- self.images = []
- self.images += [image]
-
-
-class ImagingControl:
-
- def __init__(self, openbis_instance, service_name=DEFAULT_SERVICE_NAME):
- self._openbis = openbis_instance
- self._service_name = service_name
-
- def _execute_custom_dss_service(self, parameters):
- service_id = {
- "@type": "dss.dto.service.id.CustomDssServiceCode",
- "permId": self._service_name
- }
- options = {
- "@type": "dss.dto.service.CustomDSSServiceExecutionOptions",
- "parameters": parameters
- }
- request = {
- "method": "executeCustomDSSService",
- "params": [
- self._openbis.token,
- service_id,
- options
- ],
- }
- full_url = urljoin(self._openbis._get_dss_url(), self._openbis.dss_v3)
- return self._openbis._post_request_full_url(full_url, request)
-
- def make_preview(self, perm_id: str, index: int, preview: ImagingDataSetPreview) -> ImagingDataSetPreview:
- parameters = {
- "type": "preview",
- "permId": perm_id,
- "index": index,
- "error": None,
- "preview": preview.__dict__
- }
- service_response = self._execute_custom_dss_service(parameters)
- if service_response['error'] is None:
- preview.__dict__ = service_response["preview"]
- return preview
- else:
- raise ValueError(service_response['error'])
-
- def get_export_url(self, perm_id: str, export: ImagingDataSetExport, image_index: int = 0) -> str:
- parameters = {
- "type": "export",
- "permId": perm_id,
- "index": image_index,
- "error": None,
- "url": None,
- "export": export.__dict__
- }
- service_response = self._execute_custom_dss_service(parameters)
- if service_response['error'] is None:
- return service_response['url']
- else:
- raise ValueError(service_response['error'])
-
- def get_multi_export_url(self, exports: list[ImagingDataSetMultiExport]) -> str:
- parameters = {
- "type": "multi-export",
- "error": None,
- "url": None,
- "exports": [export.__dict__ for export in exports]
- }
- service_response = self._execute_custom_dss_service(parameters)
- if service_response['error'] is None:
- return service_response['url']
- else:
- raise ValueError(service_response['error'])
-
- def single_export_download(self, perm_id: str, export: ImagingDataSetExport, image_index: int = 0, directory_path=""):
- export_url = self.get_export_url(perm_id, export, image_index)
- self._download(export_url, directory_path)
-
- def multi_export_download(self, exports: list[ImagingDataSetMultiExport], directory_path=""):
- export_url = self.get_multi_export_url(exports)
- self._download(export_url, directory_path)
-
- def _download(self, url, directory_path=""):
- get_response = requests.get(url, stream=True)
- file_name = url.split("/")[-1]
- with open(os.path.join(directory_path, file_name), 'wb') as f:
- for chunk in get_response.iter_content(chunk_size=1024):
- if chunk:
- f.write(chunk)
-
- def get_property_config(self, perm_id: str) -> ImagingDataSetPropertyConfig:
- dataset = self._openbis.get_dataset(perm_id)
- imaging_property = json.loads(dataset.props[IMAGING_CONFIG_PROP_NAME])
- return ImagingDataSetPropertyConfig.from_dict(imaging_property)
-
- def update_property_config(self, perm_id: str, config: ImagingDataSetPropertyConfig):
- dataset = self._openbis.get_dataset(perm_id)
- dataset.props[IMAGING_CONFIG_PROP_NAME] = config.to_json()
- dataset.save()
-
-
-# o = get_instance()
-#
-#
-# # imaging_preview = ImagingDataSetPreview(preview_format="png", config=config_sxm)
-# # response = get_preview('20231110130838616-26', 0, imaging_preview)
-# # print(response)
-#
-# config_export = {
-# "include": ['image', 'raw data'],
-# "image-format": 'original',
-# "archive-format": "zip",
-# "resolution": "original"
-# }
-# # imaging_export = ImagingDataSetExport(config_export)
-# # export_response = get_export('20231110130838616-26', 0, imaging_export)
-# # print(export_response)
-#
-#
-# # imaging_export1 = ImagingDataSetMultiExport('20231110130838616-26', 0, config_export)
-# # imaging_export2 = ImagingDataSetMultiExport('20231110134813653-27', 0, config_export)
-# # multi_export_response = get_multi_export([imaging_export1, imaging_export2])
-# # print(multi_export_response)
-#
-#
-# # imaging_property_config = get_property_config('20231110134813653-27')
-# # print(imaging_property_config.to_json())
-#
-# ic = ImagingControl(o)
-# perm_id = '20231110130838616-26'
-# pc = ic.get_property_config(perm_id)
-#
-#
-#
-# config_sxm_preview = {
-# "channel": "z", # usually one of these: ['z', 'I', 'dIdV', 'dIdV_Y']
-# "x-axis": [1.2, 3.0], # file dependent
-# "y-axis": [1.2, 3.0], # file dependent
-# "color-scale": [-700.0, 700.0], # file dependend
-# "colormap": "gray", # [gray, YlOrBr, viridis, cividis, inferno, rainbow, Spectral, RdBu, RdGy]
-# "scaling": "linear", # ['linear', 'logarithmic']
-# # "mode": 3 # uncomment this if you want to generate random pixel image generation
-# }
-#
-# # imaging_preview = ImagingDataSetPreview(preview_format="png", config=config_sxm_preview)
-# #
-# # preview = ic.make_preview(perm_id, 0, imaging_preview)
-# # pc.images[0].add_preview(preview)
-# # ic.update_property_config(perm_id, pc)
-# #
-# # print(ic.get_property_config(perm_id))
-#
-#
-#
-# config_export = {
-# "include": ['image', 'raw data'],
-# "image-format": 'original',
-# "archive-format": "zip",
-# "resolution": "original"
-# }
-# imaging_export = ImagingDataSetExport(config_export)
-# ic.single_export_download(perm_id, imaging_export, 0, '/home/alaskowski/PREMISE')
-
-
-
-
-
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/python/tests/test_imaging.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/python/tests/test_imaging.py
deleted file mode 100644
index 05b18b5f8343058bd3e75e620d00061693d3b297..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/python/tests/test_imaging.py
+++ /dev/null
@@ -1,119 +0,0 @@
-# Copyright ETH 2023 Zürich, Scientific IT Services
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-import unittest
-import imaging.imaging as imaging
-from unittest.mock import MagicMock
-import json
-
-IMAGING_CONFIG_PROP_NAME = "$IMAGING_DATA_CONFIG".lower()
-
-PROPER_CONFIG = {
- "config": {
- "adaptor": "some.adaptor.class.MyAdaptorClass",
- "version": 1.0,
- "speeds": [1, 2, 5],
- "resolutions": ["150dpi", "300dpi"],
- "playable": True,
- "exports": [{
- "label": "Archive",
- "type": "Dropdown",
- "values": ["zip", "tar.gz"],
- "multiselect": False,
- "metaData": {}
- }],
- "inputs": [{
- "label": "Option 1",
- "section": "section",
- "type": "Dropdown",
- "values": ["a", "b", "c"],
- "multiselect": True,
- "playable": False,
- "metaData": {}
- }, {
- "label": "Option 2",
- "section": "section",
- "type": "Slider",
- "unit": "cm",
- "range": ["1", "2", "0.1"],
- "multiselect": False,
- "playable": True,
- "speeds": [1, 2, 5],
- "metaData": {}
- }, {
- "label": "Option 2",
- "section": "section",
- "type": "Range",
- "multiselect": False,
- "playable": False,
- "visibility": [{
- "label": "Option 1",
- "values": ["a", "b"],
- "range": ["1", "2", "0.1"],
- "unit": "mm"
- }, {
- "label": "Option 1",
- "values": ["c"],
- "range": ["0", "100", "1"],
- "unit": "px"
- }],
- "metaData": {}
- }],
- "metadata": {}
- },
- "images": [{
- "previews": [{
- "config": {},
- "format": "png",
- "bytes": "base64_encoded_bytes",
- "show": False,
- "metadata": {}
- }],
- "config": {},
- "metadata": {}
- }]
-}
-
-
-class ImagingTestCase(unittest.TestCase):
-
- def setUp(self):
- self.dataset_mock = MagicMock()
- self.set_dataset_config(PROPER_CONFIG)
-
- self.openbis_mock = MagicMock()
- self.openbis_mock.get_dataset.return_value = self.dataset_mock
-
- self.imaging_control = imaging.ImagingControl(self.openbis_mock)
-
- def set_dataset_config(self, config):
- json_config = json.dumps(config)
- self.dataset_mock.props = {IMAGING_CONFIG_PROP_NAME: json_config}
-
- def test_get_proper_config(self):
- config = self.imaging_control.get_property_config('some_perm_id')
- assert len(config.images) == 1
- assert len(config.images[0].previews) == 1
-
- def test_get_empty_config(self):
- self.set_dataset_config(None)
- self.assertRaises(AssertionError, self.imaging_control.get_property_config, 'some_perm_id')
-
- #TODO expand tests
-
-
-
-if __name__ == '__main__':
- unittest.main()
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/sourceTest/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingServiceTest.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/sourceTest/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingServiceTest.java
deleted file mode 100644
index 9327e229c57d8619397e9f039f2ed07d6949bc55..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/sourceTest/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingServiceTest.java
+++ /dev/null
@@ -1,116 +0,0 @@
-/*
- * Copyright ETH 2023 Zürich, Scientific IT Services
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging;
-
-import static org.junit.Assert.fail;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetKind;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetCreation;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.PhysicalDataCreation;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.delete.DataSetDeletionOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.FileFormatTypePermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.ProprietaryStorageFormatPermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.RelativeLocationLocatorTypePermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.DataStorePermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.CustomDSSServiceExecutionOptions;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.id.CustomDssServiceCode;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.id.ICustomDSSServiceId;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container.ImagingPreviewContainer;
-import org.testng.annotations.Test;
-import org.junit.Assert.*;
-
-import java.util.*;
-
-
-public class ImagingServiceTest //extends AbstractFileTest
-{
-
-
- @Test
- public void testImagingService() throws Exception
- {
-// fail();
-// String sessionToken = as.login(TEST_USER, PASSWORD);
-//
-// DataSetPermId dataSetPermId = new DataSetPermId("TEST-IMAGING-" + UUID.randomUUID().toString());
-// createDirectories(workingDirectory, new HashSet<>(List.of("dss-root", "dss-root/store", "dss-root/store/1",
-// "dss-root/store/1/" + dataSetPermId.getPermId())));
-// createFiles(workingDirectory, List.of("dss-root/store/1/" + dataSetPermId.getPermId() + "/file1.txt"));
-//
-// try
-// {
-// PhysicalDataCreation physicalCreation = new PhysicalDataCreation();
-// physicalCreation.setLocation(dataSetPermId.getPermId());
-// physicalCreation.setFileFormatTypeId(new FileFormatTypePermId("TIFF"));
-// physicalCreation.setLocatorTypeId(new RelativeLocationLocatorTypePermId());
-// physicalCreation.setStorageFormatId(new ProprietaryStorageFormatPermId());
-//
-// DataSetCreation creation = new DataSetCreation();
-// creation.setCode(dataSetPermId.getPermId());
-// creation.setDataSetKind(DataSetKind.PHYSICAL);
-// creation.setTypeId(new EntityTypePermId("IMAGING_DATA"));
-// creation.setExperimentId(new ExperimentIdentifier("/TEST-SPACE/TEST-PROJECT/EXP-SPACE-TEST"));
-// creation.setDataStoreId(new DataStorePermId("STANDARD"));
-// creation.setPhysicalData(physicalCreation);
-// creation.setProperty("$IMAGING_DATA_CONFIG", "{\"config\" : { \"@type\" : \"dss.dto.imaging.ImagingDataSetConfig\", \"adaptor\" : \"ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.adaptor.ImagingDataSetExampleAdaptor\" } }");
-//
-//
-// List<DataSetPermId> ds = as.createDataSets(sessionToken, Arrays.asList(creation));
-// DataSetPermId pds = ds.get(0);
-//
-// ICustomDSSServiceId serviceId = new CustomDssServiceCode("imaging");
-//
-// Map<String, Object> map = Map.of("@type", "dss.dto.imaging.ImagingDataSetPreview",
-// "config", Map.of("Dimension 1", new Integer[] {1,2}));
-//
-// CustomDSSServiceExecutionOptions options = new CustomDSSServiceExecutionOptions();
-// options.withParameter("type", "preview");
-// options.withParameter("permId", pds.getPermId());
-// options.withParameter("index", 0);
-// options.withParameter("preview", map);
-// Object executionResult = dss.executeCustomDSSService(sessionToken, serviceId, options);
-//
-//// assertTrue(executionResult instanceof ImagingPreviewContainer);
-//// ImagingPreviewContainer result = (ImagingPreviewContainer) executionResult;
-////
-//// assertNotNull(result.getPreview().getBytes());
-// }
-// finally
-// {
-// DataSetDeletionOptions options = new DataSetDeletionOptions();
-// options.setReason("cleanup");
-// as.deleteDataSets(sessionToken, Arrays.asList(dataSetPermId), options);
-// as.logout(sessionToken);
-// }
- }
-
-
-
-
-
-
-
-
-
-
-
-
-}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/sourceTest/java/tests.xml b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/sourceTest/java/tests.xml
deleted file mode 100644
index adca2f5bb61f4ab8b7dbd1fd9a9095959f9f7422..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/sourceTest/java/tests.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<suite name="All" verbose="2">
- <test name="All" annotations="JDK">
- <groups>
- <run>
- <exclude name="broken" />
- </run>
- </groups>
- <packages>
- <package name="ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.*" />
- </packages>
- </test>
-</suite>
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py
deleted file mode 100644
index 6b1c598587aa6ba994e31233e719ccbe49052e67..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py
+++ /dev/null
@@ -1,119 +0,0 @@
-import numpy
-from PIL import Image
-import io
-import base64
-import sys
-import json
-import os
-import sys
-from spmpy_terry import spm # <--- class spm defines objects of type spm with their attributes and class functions
-import spmpy_terry as spmpy # <--- spmpy has other methods
-from datetime import datetime
-
-import matplotlib.pyplot as plt
-# %matplotlib inline
-
-
-def load_image(path):
- return spm(path)
-
-
-def get_lock_in(img):
- param_name = 'lock-in>lock-in status'
- param = img.get_param(param_name)
- return param
-
-
-def get_channel(img, channel_name = 'z'):
- # channel_name = 'z'
- channel = img.get_channel(channel_name)
- return channel
-
-
-file = sys.argv[1]
-image_params = json.loads(sys.argv[2])
-params = json.loads(sys.argv[3])
-meta_data = json.loads(sys.argv[4])
-format = sys.argv[5]
-
-
-folder_dir = os.path.join(file, 'original')
-file_path = os.path.join(folder_dir, os.listdir(folder_dir)[0])
-# print(file_path)
-
-
-def generate_random_image(height, width):
- imarray = numpy.random.rand(height,width,3) * 255
- im = Image.fromarray(imarray.astype('uint8')).convert('RGBA')
- img_byte_arr = io.BytesIO()
- im.save(img_byte_arr, format=format)
- img_byte_arr = img_byte_arr.getvalue()
- encoded = base64.b64encode(img_byte_arr)
- return encoded
-
-
-def get_dat_image(channel_x, channel_y, x_axis, y_axis, colormap, scaling, grouping, print_legend):
- specs = spmpy.importall(folder_dir, '', 'spec')
-
- for spec in specs:
- date_time = spec.get_param('Saved Date')
- spec.date_time = datetime.strptime(date_time, "%d.%m.%Y %H:%M:%S")
-
- # sort measurements according to date
- specs.sort(key=lambda d: d.date_time)
- specs_sub = list(filter(lambda spec:spec.name in grouping, specs))
-
- print_legend = print_legend
- show = False
- fig = spmpy.specs_plot(specs_sub, channelx=channel_x, channely=channel_y, direction='forward',
- print_legend=print_legend, show=show, colormap=colormap, scaling=scaling,
- x_axis=x_axis, y_axis=y_axis)
-
- img_byte_arr = io.BytesIO()
- plt.savefig(img_byte_arr, format=format)
- img_byte_arr = img_byte_arr.getvalue()
- encoded = base64.b64encode(img_byte_arr)
- return encoded
-
-
-
-
-
-print(params)
-if 'mode' in params:
- if params['mode'] == '1':
- print(generate_random_image(640, 640))
- elif params['mode'] == '2':
- parameters = dict(
- channel_x=params['channel x'],
- channel_y=params['channel y'],
- x_axis=[float(x) for x in params['x-axis']],
- y_axis=[float(x) for x in params['y-axis']],
- colormap=params['colormap'],
- scaling=params['scaling'],
- grouping=params['grouping']
- )
- if "color" in params:
- parameters['color'] = params['color']
- if "print_legend" in params:
- parameters['print_legend'] = params['print_legend'].upper() == "TRUE"
- else:
- parameters['print_legend'] = True
- print(get_dat_image(**parameters))
-else:
- parameters = dict(
- channel_x=params['channel x'],
- channel_y=params['channel y'],
- x_axis=[float(x) for x in params['x-axis']],
- y_axis=[float(x) for x in params['y-axis']],
- colormap=params['colormap'],
- scaling=params['scaling'],
- grouping=params['grouping']
- )
- if "color" in params:
- parameters['color'] = params['color']
- if "print_legend" in params:
- parameters['print_legend'] = params['print_legend'].upper() == "TRUE"
- else:
- parameters['print_legend'] = True
- print(get_dat_image(**parameters))
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py
deleted file mode 100644
index 476d27f5a0a1b8e2499b30121a5bbd2aaf7ecc5f..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py
+++ /dev/null
@@ -1,100 +0,0 @@
-import numpy
-from PIL import Image
-import io
-import base64
-import sys
-import json
-import os
-import sys
-from spmpy_terry import spm # <--- class spm defines objects of type spm with their attributes and class functions
-import spmpy_terry as spmpy # <--- spmpy has other methods
-
-import matplotlib.pyplot as plt
-# %matplotlib inline
-
-
-class NumpyEncoder(json.JSONEncoder):
- def default(self, obj):
- if isinstance(obj, numpy.ndarray):
- return obj.tolist()
- return json.JSONEncoder.default(self, obj)
-
-def load_image(path):
- return spm(path)
-
-
-def get_lock_in(img):
- param_name = 'lock-in>lock-in status'
- param = img.get_param(param_name)
- return param
-
-
-def get_channel(img, channel_name = 'z'):
- # channel_name = 'z'
- channel = img.get_channel(channel_name)
- return channel
-
-print("SYS.ARGV:" + str(sys.argv))
-file = sys.argv[1]
-image_params = json.loads(sys.argv[2])
-params = json.loads(sys.argv[3])
-meta_data = json.loads(sys.argv[4])
-format = sys.argv[5]
-
-
-folder_dir = os.path.join(file, 'original')
-file_path = os.path.join(folder_dir, os.listdir(folder_dir)[0])
-
-
-def generate_random_image(height, width):
- imarray = numpy.random.rand(height,width,3) * 255
- im = Image.fromarray(imarray.astype('uint8')).convert('RGBA')
- img_byte_arr = io.BytesIO()
- im.save(img_byte_arr, format='PNG')
- img_byte_arr = img_byte_arr.getvalue()
- encoded = base64.b64encode(img_byte_arr)
- return encoded
-
-
-def get_sxm_image(channel_name, x_axis, y_axis, scaling, color_scale, colormap, colormap_scaling):
- img = load_image(file_path)
- img_byte_arr = io.BytesIO()
-
- log = False
- if scaling == 'logarithmic':
- log = True
- fig = img.plot(show=False, show_params=False, channel=channel_name, log=log, cmap=colormap,
- color_scale=color_scale, x_axis=x_axis, y_axis=y_axis, colormap_scaling=colormap_scaling)
- plt.savefig(img_byte_arr, format=format)
-
- img_byte_arr = img_byte_arr.getvalue()
- encoded = base64.b64encode(img_byte_arr)
- print_params = img.print_params(show=False).split('\n')
- print_params = {x: y for x, y in (s.split(':') for s in print_params)}
- print_params = json.dumps(print_params)
- print(f'PARAMS={print_params}')
- header = json.dumps(img.header, cls=NumpyEncoder)
- print(f'HEADER={header}')
-
- return encoded
-
-def sxm_mode(parameters):
- channel = parameters['channel']
- x_axis = [float(x) for x in parameters['x-axis']]
- y_axis = [float(x) for x in parameters['y-axis']]
- color_scale = [float(x) for x in parameters['color-scale']]
- colormap = parameters['colormap']
- scaling = parameters['scaling']
- colormap_scaling = False
- if "colormap_scaling" in parameters:
- colormap_scaling = parameters['colormap_scaling'].upper() == "TRUE"
- print(f'{get_sxm_image(channel, x_axis, y_axis, scaling, color_scale, colormap, colormap_scaling)}')
-
-print(params)
-if 'mode' in params:
- if params['mode'] == '3':
- print(f'{generate_random_image(256, 256)}')
- elif params['mode'] == '5':
- sxm_mode(params)
-else:
- sxm_mode(params)
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/plugin.properties b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/plugin.properties
deleted file mode 100644
index a669c47e3ac56fd9df98e0c6dfb85f0f2795071a..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/plugin.properties
+++ /dev/null
@@ -1,8 +0,0 @@
-label = PremiseImagingService
-
-class2 = ch.ethz.sis.openbis.generic.server.dss.plugins.PingPongService
-class = ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.ImagingService
-
-python3-path = /home/alaskowski/virtualenv_python/bin/python3
-nanonis-sxm = nanonis_sxm.py
-nanonis-dat = nanonis_dat.py
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/spmpy_terry.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/spmpy_terry.py
deleted file mode 100644
index 57702f4aef451c718be269e712179144f2ec8499..0000000000000000000000000000000000000000
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/spmpy_terry.py
+++ /dev/null
@@ -1,970 +0,0 @@
- # -*- coding: utf-8 -*-
-"""
-Created on Tue Jan 3 15:13:13 2017
-
-@author: Bruno Schuler
-"""
-
-##############################################
-# spm_matrix class
-##############################################
-
-# This module provides functions to load and display Nanonis files
-
-# requires packages:
-# pip install numpy
-# pip install six
-# pip install nanonispy
-# pip install spiepy
-
-import os as os
-import numpy as np
-import nanonispy as nap
-import spiepy
-import warnings
-import matplotlib.pyplot as plt
-import matplotlib.pylab as pl
-
-class spm:
-
- #Dictionary Channels
- ChannelName = ['LI_Demod_1_X','LI_Demod_1_Y','Z','Current','Bias','Frequency_Shift','Amplitude','Excitation','Temperature_1',
- 'Bias (V)','Bias calc (V)', 'Bias [bwd] (V)', 'Current (A)','Current [bwd] (A)','Amplitude (m)',
- 'Amplitude [bwd] (m)', 'Excitation (V)', 'Excitation [bwd] (V)', 'Frequency Shift (Hz)', 'Frequency Shift [bwd] (Hz)',
- 'LI Demod 1 X (A)','LI Demod 1 X (A) [bwd] (A)','PMT (V)','Counter 1 (Hz)','Counter_1', 'Z rel (m)', 'Z (m)','Time (s)',
- 'Delay Sampling (s)','LI Demod 0 X (V)','LI Demod 0 Y (V)','LI Demod 3 X (A)','LI Demod 3 Y (A)',
- 'Position Phase1 (m)','Rotation1 (deg)','Rotation2 (deg)','Rotation (deg)','Index']
- ChannelNickname = ['dIdV','dIdV_Y','z','I','V','df','A','exc','T1',
- 'V', 'V', 'V_bw' ,'I','I_bw','A',
- 'A_bw', 'exc','exc_bw','df','df_bw',
- 'dIdV','dIdV_bw','PMT','counter','counter', 'zrel','zspec','t',
- 'Delay','EOS','EOS_Y','I_THz','I_THz_Y',
- 'Phase','Rot1','Rot2','Rot','Index']
- ChanneliScaling = [10**12,10**12,10**9,10**12,1,1,10**9,1,1,
- 1,1,1,10**12,10**12,10**9,
- 10**9,1,1,1,1,1,
- 1,1,1,1,10**12,10**9,1,
- 10**12,1,1,10**12,10**12,
- 10**3,1,1,1,1]
- ChannelUnit = ['pS','pS','nm','pA','V','Hz','nm','V','K',
- 'V','V','V','pA','pA','nm',
- 'nm','V','V','Hz','Hz','a.u.',
- 'a.u.','V','Hz','Hz','pm','nm','s',
- 'ps','V','V','pA','pA',
- 'mm','deg','deg','deg','N']
-
- global SignalsListReference
- SignalsListReference = []
-
- for (chName,chNickname,chScaling,chUnit) in zip(ChannelName,ChannelNickname,ChanneliScaling,ChannelUnit):
- SignalsListReference.append({'ChannelName': chName, 'ChannelNickname': chNickname , 'ChannelScaling': chScaling, 'ChannelUnit': chUnit})
-
- del ChannelName,ChanneliScaling,ChannelUnit
- del chName,chNickname,chScaling,chUnit
-
- #Dictionary Parameters
- ParamName = ['X (m)','Y (m)','Z (m)','bias','z-controller>setpoint','scan_angle','Comments','Comment01',
- 'Lock-in>Amplitude','Lock-in>Reference phase D1 (deg)','Lock-in>Frequency (Hz)','Temperature 2>Temperature 2 (K)',
- 'Current>Current (A)','Bias>Bias (V)','z-controller>tiplift (m)',
- 'Parameter>Delay Sampling (s)','Parameter>Delay PP1 (s)','Parameter>Delay PP2 (s)','Parameter>Angle Rot1 (deg)','Parameter>Angle Rot2 (deg)','Parameter>Position Phase1 (m)','Parameter>Position_Phase1 (m)']
- ParamNickname = ['x','y','z','V','setpoint','angle','comment','comment_spec',
- 'lockin_amplitude','lockin_phase','lockin_frequency','temperature',
- 'setpoint_spec','V_spec','z_offset',
- 'Sampling','PP1','PP2','Rot1','Rot2','Phase','Phase_depricated']
- ParamScaling = [10**9,10**9,10**9,1,10**12,1,'na','na',
- 10**3,1,1,1,
- 10**12,1,10**9,
- 10**12,10**12,10**12,1,1,10**3,10**3] # na if not a numeric value
- ParamUnit = ['nm','nm','nm','V','pA','°','','',
- 'mV','°','Hz','K',
- 'pA','V','nm',
- 'ps','ps','ps','deg','deg','mm','mm']
-
-
- global ParamListReference
- ParamListReference = []
-
- for (paName,paNickname,paScaling,paUnit) in zip(ParamName,ParamNickname,ParamScaling,ParamUnit):
- ParamListReference.append({'ParamName': paName, 'ParamNickname': paNickname, 'ParamScaling': paScaling, 'ParamUnit': paUnit})
-
- del ParamName,ParamScaling,ParamUnit
- del paName,paNickname,paScaling,paUnit
-
- # constructor
- def __init__(self,path):
- #import os as os
- #import numpy as np
- #import nanonispy as nap
-
-
- # self.path = path.replace('//', '/')
- abspath = os.path.abspath(path)
- self.path = '/'.join(abspath.split('\\')[-4:])
- self.name = self.path.split('/')[-1]
- file_extension = os.path.splitext(path)[1]
-
- if file_extension == '.sxm':
- self.napImport = nap.read.Scan(path)
- self.type = 'scan'
- elif file_extension == '.dat':
- self.napImport = nap.read.Spec(path)
- self.type = 'spec'
- else:
- print('Datatype not supported.')
- return;
-
- ch = []
- for key in self.napImport.signals:
- try:
- ch.append([d['ChannelName'] for d in SignalsListReference].index(key))
- except:
- pass;
-
- self.SignalsList = [SignalsListReference[i] for i in ch] #List of all recorded channels
- self.channels = [c['ChannelNickname'] for c in self.SignalsList]
- self.header = self.napImport.header
-
-
- def __repr__(self):
- return self.path
-
- #get channel
- def get_channel(self,channel,direction = 'forward', flatten = False, offset = False,zero = False):
-
- #import spiepy
- #import numpy as np
-
- if self.type == 'scan':
- chNum = [d['ChannelNickname'] for d in self.SignalsList].index(channel)
- im = self.napImport.signals[self.SignalsList[chNum]['ChannelName']][direction]
- im = im *self.SignalsList[chNum]['ChannelScaling']
-
- if flatten:
- if ~np.isnan(np.sum(im)):
- im, _ = spiepy.flatten_xy(im)
- else:
- m,n = np.shape(im)
- i = np.argwhere(np.isnan(im))[0,0]
- im_cut = im[:i-1,:]
- im, _ = spiepy.flatten_xy(im_cut)
- empty = np.full((m-i,n),np.nan)
- im = np.vstack((im,empty))
-
- warnings.warn('NaN values in image')
- #im-np.nanmean(im)
-
- if offset:
- im = im-np.mean(im)
- if zero:
- im = im+abs(np.min(im))
-
- unit = self.SignalsList[chNum]['ChannelUnit']
-
- return (im,unit)
-
- elif self.type == 'spec':
-
- if direction == 'backward':
- channel = channel + '_bw';
- #print(channel)
-
- chNum = [d['ChannelNickname'] for d in self.SignalsList].index(channel)
- data = self.napImport.signals[self.SignalsList[chNum]['ChannelName']]
- data = data*self.SignalsList[chNum]['ChannelScaling']
- unit = self.SignalsList[chNum]['ChannelUnit']
-
- return (data,unit)
-
- return
-
- #get parameter
- def get_param(self,param):
-
- if any(d['ParamNickname'] == param for d in ParamListReference):
- paNum = [d['ParamNickname'] for d in ParamListReference].index(param)
-
- if ParamListReference[paNum]['ParamScaling'] == 'na':
- return self.napImport.header[ParamListReference[paNum]['ParamName']]
- else:
- return (float(self.napImport.header[ParamListReference[paNum]['ParamName']])*ParamListReference[paNum]['ParamScaling'],ParamListReference[paNum]['ParamUnit'])
-
-
- elif param == 'width' or param == 'height':
- # height, width = self.get_param('scan_range')
- # height, width = [height*10**9, width*10**9]
- scanfield = self.get_param('scan>scanfield')
- width, height = float(scanfield.split(';')[2])*10**9, float(scanfield.split(';')[3])*10**9
-
- return (eval(param),'nm')
-
-
- else:
- if param in self.napImport.header.keys():
- return self.napImport.header[param]
- else:
- return
-
-
-
- # print essential parameters for plotting
- def print_params(self, show = True):
-
- # import numpy as np
-
- label = []
-
- if self.type == 'scan':
- fb_enable = self.get_param('z-controller>controller status')
- fb_ctrl = self.get_param('z-controller>controller name')
- bias = self.get_param('V')
- set_point = self.get_param('setpoint')
- height = self.get_param('height')
- width = self.get_param('width')
- angle = self.get_param('angle')
- z_offset = self.get_param('z_offset')
- comment = self.get_param('comments')
-
-
-
- if fb_enable == 'OFF':
- label.append('constant height')
- label.append('z-offset: %.3f%s' % z_offset)
-
- if np.abs(bias[0])<0.1:
- bias = list(bias)
- bias[0] = bias[0]*1000
- bias[1] = 'mV'
- bias = tuple(bias)
-
- label.append('I: %.0f%s' % set_point)
- label.append('bias: %.2f%s' % bias)
- label.append('size: %.1f%s x %.1f%s (%.0f%s)' % (width+height+angle))
- label.append('comment: %s' % comment)
-
-
- elif self.type == 'spec':
-
- fb_enable = self.get_param('Z-Ctrl hold')
- set_point = self.get_param('setpoint_spec')
- bias = self.get_param('V_spec')
- #lockin_status = self.get_param('Lock-in>Lock-in status')
- lockin_amplitude = self.get_param('lockin_amplitude')
- lockin_phase= self.get_param('lockin_phase')
- lockin_frequency= self.get_param('lockin_frequency')
- comment = self.get_param('comment_spec')
-
-
- #if lockin_status == 'ON':
- label.append('lockin: A = %.0f%s (θ = %.0f%s, f = %.0f%s)' % (lockin_amplitude+lockin_phase+lockin_frequency))
-
-
- if fb_enable == 'FALSE':
- label.append('feedback: on')
-
- elif fb_enable == 'TRUE':
- label.append('feedback: off')
-
-
- label.append('setpoint: I = %.0f%s, V = %.1f%s' % (set_point+bias))
-
- label.append('comment: %s' % comment)
-
- label.append('path: %s' % self.path)
- label = '\n'.join(label)
-
- if show:
- print(label)
-
- return label
-
-
-
- # plot
- def plot(self, **params):
- import numpy as np
- #import matplotlib as ml
- import matplotlib.pyplot as plt
- from matplotlib.colors import LogNorm
-
- #cmaps = sorted(m for m in plt.cm.datad)
- # ['Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', 'BuGn', 'BuGn_r', 'BuPu', 'BuPu_r', 'CMRmap', 'CMRmap_r', 'Dark2', 'Dark2_r', 'GnBu', 'GnBu_r', 'Greens', 'Greens_r', 'Greys', 'Greys_r', 'OrRd', 'OrRd_r', 'Oranges', 'Oranges_r', 'PRGn', 'PRGn_r', 'Paired', 'Paired_r', 'Pastel1', 'Pastel1_r', 'Pastel2', 'Pastel2_r', 'PiYG', 'PiYG_r', 'PuBu', 'PuBuGn', 'PuBuGn_r', 'PuBu_r', 'PuOr', 'PuOr_r', 'PuRd', 'PuRd_r', 'Purples', 'Purples_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdPu', 'RdPu_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r', 'Reds', 'Reds_r', 'Set1', 'Set1_r', 'Set2', 'Set2_r', 'Set3', 'Set3_r', 'Spectral', 'Spectral_r', 'Wistia', 'Wistia_r', 'YlGn', 'YlGnBu', 'YlGnBu_r', 'YlGn_r', 'YlOrBr', 'YlOrBr_r', 'YlOrRd', 'YlOrRd_r', 'afmhot', 'afmhot_r', 'autumn', 'autumn_r', 'binary', 'binary_r', 'bone', 'bone_r', 'brg', 'brg_r', 'bwr', 'bwr_r', 'cool', 'cool_r', 'coolwarm', 'coolwarm_r', 'copper', 'copper_r', 'cubehelix', 'cubehelix_r', 'flag', 'flag_r', 'gist_earth', 'gist_earth_r', 'gist_gray', 'gist_gray_r', 'gist_heat', 'gist_heat_r', 'gist_ncar', 'gist_ncar_r', 'gist_rainbow', 'gist_rainbow_r', 'gist_stern', 'gist_stern_r', 'gist_yarg', 'gist_yarg_r', 'gnuplot', 'gnuplot2', 'gnuplot2_r', 'gnuplot_r', 'gray', 'gray_r', 'hot', 'hot_r', 'hsv', 'hsv_r', 'jet', 'jet_r', 'nipy_spectral', 'nipy_spectral_r', 'ocean', 'ocean_r', 'pink', 'pink_r', 'prism', 'prism_r', 'rainbow', 'rainbow_r', 'seismic', 'seismic_r', 'spectral', 'spectral_r', 'spring', 'spring_r', 'summer', 'summer_r', 'terrain', 'terrain_r', 'winter', 'winter_r']
-
- #ml.interactive(0)
-
- if self.type == 'scan':
-
- if 'channel' in params:
- channel = params['channel']
- else:
- channel = self.channels[0]
-
- if 'direction' in params:
- direction = params['direction']
- else:
- direction = 'forward'
-
- if 'flatten' in params:
- flatten = params['flatten']
- else:
- flatten = False
-
- if 'offset' in params:
- offset = params['offset']
- else:
- offset = False
-
- if 'cmap' in params:
- cmap = params['cmap']
- else:
- cmap = 'gray'
-
- if 'clim' in params:
- clim = params['clim']
- else:
- clim = False
-
- if 'log' in params:
- log = params['log']
- else:
- log = False
-
- if 'show_params' in params:
- show_params = params['show_params']
- else:
- show_params = False
-
- if 'show' in params:
- show = params['show']
- else:
- show = True
-
- # PREMISE - specific params
-
- if 'hide' in params:
- hide = params['hide']
- else:
- hide = False
-
- if 'color_scale' in params:
- color_scale = params['color_scale']
- else:
- color_scale = False
-
- if 'x_axis' in params:
- x_axis = params['x_axis']
- else:
- x_axis = False
-
- if 'y_axis' in params:
- y_axis = params['y_axis']
- else:
- y_axis = False
-
- if 'colormap_scaling' in params:
- colormap_scaling = params['colormap_scaling']
- else:
- colormap_scaling = False
-
-
-
- (chData,chUnit) = self.get_channel(channel, direction = direction, flatten=flatten, offset=offset);
-
- if direction == 'backward':
- chData = np.fliplr(chData)
-
- width = self.get_param('width')
- height = self.get_param('height')
- pix_y,pix_x = np.shape(chData)
-
- # fig = plt.figure(figsize=(6, 4))
- fig = plt.figure()#figsize=(6,4))
-
-
- ImgOrigin = 'lower'
- if self.get_param('scan_dir') == 'down':
- ImgOrigin = 'upper'
-
- if color_scale:
- chData = np.clip(chData, color_scale[0], color_scale[1])
-
- if x_axis and y_axis:
- plt.ylim(y_axis[0], y_axis[1])
- plt.xlim(x_axis[0], x_axis[1])
- # plt.axis([x_axis[0], x_axis[1], y_axis[0], y_axis[1]])
-
- plot_params = dict(
- X = np.abs(chData) if log else chData,
- aspect = 'equal',
- extent = [0,width[0],0,height[0]],
- cmap = cmap,
- origin = ImgOrigin,
- interpolation = 'none'
- )
- if log:
- plot_params['norm'] = LogNorm()
-
- if colormap_scaling:
- min_x = x_axis[0]
- max_x = x_axis[1]
- min_y = y_axis[0]
- max_y = y_axis[1]
-
- shape = chData.shape
- minx = int(np.floor(shape[0] * min_x / width[0]))
- maxx = int(np.ceil(shape[0] * max_x / width[0]))
- miny = int(np.floor(shape[1] * min_y / height[0]))
- maxy = int(np.ceil(shape[1] * max_y / height[0]))
-
- mini = np.min(chData[minx:maxx, miny:maxy])
- maxi = np.max(chData[minx:maxx, miny:maxy])
-
- mini = int(mini*100)/100
- maxi = int(maxi*100)/100
- plot_params['vmin'] = mini
- plot_params['vmax'] = maxi
-
- im = plt.imshow(**plot_params)
-
- # if log:
- # im = plt.imshow(np.abs(chData), aspect = 'equal', extent = [0,width[0],0,height[0]], cmap = cmap, norm=LogNorm(), origin = ImgOrigin)
- # else:
- # im = plt.imshow(chData, aspect = 'equal',extent = [0,width[0],0,height[0]], cmap = cmap, origin = ImgOrigin)
-
-
- if clim:
- plt.clim(clim)
-
-
- # im.axes.set_xticks([0,width[0]])
- # im.axes.set_xticklabels([0,np.round(width[0],2)])
- # im.axes.set_yticks([0,height[0]])
- # im.axes.set_yticklabels([0,np.round(height[0],2)])
-
- if show_params:
- title = self.print_params(show = False);
- else:
- title = self.path
-
- if not hide:
- # plt.title(title + '\n', loc='left')
- plt.xlabel('x (%s)' % width[1])
- plt.ylabel('y (%s)' % height[1])
- print(f'AXES={im.axes}')
- cbar = plt.colorbar(im)#,fraction=0.046, pad=0.02, format='%.2g',shrink = 0.5,aspect=10)
- cbar.set_label('channel:%s (%s)' % (channel,chUnit))
-
- if show:
- plt.show()
- # else:
- # plt.close(fig)
-
- return fig
-
-
-
- elif self.type == 'spec':
-
-
- if 'channelx' in params:
- channelx = params['channelx']
- else:
- channelx = self.channels[0]
-
- if 'channely' in params:
- channely = params['channely']
- else:
- channely = self.channels[1]
-
- if 'direction' in params:
- direction = params['direction']
- else:
- direction = direction = 'forward'
-
- if 'log' in params:
- log = params['log']
- else:
- log = False
-
- if 'loglog' in params:
- loglog = params['loglog']
- else:
- loglog = False
-
-
- if 'show_params' in params:
- show_params = params['show_params']
- else:
- show_params = False
-
- if 'show' in params:
- show = params['show']
- else:
- show = True
-
-
- (x_data,x_unit) = self.get_channel(channelx,direction=direction)
- (y_data,y_unit) = self.get_channel(channely,direction=direction)
-
-
- fig = plt.figure(figsize=(6,4))
-
- if log:
- plt.semilogy(x_data,np.abs(y_data))
-
- elif loglog:
- plt.loglog(np.abs(x_data),np.abs(y_data))
-
- else:
- plt.plot(x_data,y_data)
-
-
- if show_params:
- title = self.print_params(show = False);
- else:
- title = self.path
-
- plt.title(title + '\n', loc='left')
-
- plt.xlabel('%s (%s)' % (channelx,x_unit))
- plt.ylabel('%s (%s)' % (channely,y_unit))
-
- if show:
- plt.show()
- else:
- plt.close(fig)
-
- return fig
-
-
-
-
-
-##############################################
-# functions for spm class
-##############################################
-
-
-# import all files in folder as list of spm objects
-def importall(FilePath,FilePrefix = '',ImportOnly = '' ):
-
- from os import walk
-
- files = []
- NumSpec = 0
- NumScan = 0
-
-
- for root, dirs, filenames in walk(FilePath):
- for file in filenames:
- if file.endswith(".sxm") and file.startswith(FilePrefix):
- if not(ImportOnly == 'spec'):
- files.append(spm(root + '/' + file))
- NumScan = NumScan + 1
- elif file.endswith(".dat") and file.startswith(FilePrefix):
- if not(ImportOnly == 'scan'):
- files.append(spm(root + '/' + file))
- NumSpec = NumSpec + 1
-
- print(str(len(files)) + ' files imported; ' + str(NumScan) + ' scan(s) and ' + str(NumSpec) + ' spectra')
-
- return files
-
-# def importspecific(FilePath,FileList,FilePrefix = '',ImportOnly = '' ):
-
-# from os import walk
-
-# files = []
-# NumSpec = 0
-# NumScan = 0
-
-
-# for root, dirs, filenames in walk(FilePath):
-# for file in filenames:
-# if (file in FileList):
-# if file.endswith(".sxm") and file.startswith(FilePrefix):
-# if not(ImportOnly == 'spec'):
-# files.append(spm(root + '/' + file))
-# NumScan = NumScan + 1
-# elif file.endswith(".dat") and file.startswith(FilePrefix):
-# if not(ImportOnly == 'scan'):
-# files.append(spm(root + '/' + file))
-# NumSpec = NumSpec + 1
-
-# print(str(len(files)) + ' files imported; ' + str(NumScan) + ' scan(s) and ' + str(NumSpec) + ' spectra')
-
-# return files
-
-
-
-
-def specs_plot(specs,**params):
-# plot spectra in list
-
- #import matplotlib.pyplot as plt
-
- if 'channelx' in params:
- channelx = params['channelx']
- else:
- channelx = specs[0].channels[0]
-
- if 'channely' in params:
- channely = params['channely']
- else:
- channely = specs[0].channels[1]
-
- if 'direction' in params:
- direction = params['direction']
- else:
- direction = list(specs[0].data.keys())[0]
-
- if 'color' in params:
- color = params['color']
- else:
- color = pl.cm.rainbow(np.linspace(0,1,len(specs)))
- if 'print_legend' in params:
- print_legend = params['print_legend']
- else:
- print_legend = False
- if 'offset' in params:
- offset = params['offset']
- else:
- offset = 0
-
- # PREMISE specific
- if 'show' in params:
- show = params['show']
- else:
- show = True
-
- if 'colormap' in params:
- colormap = params['colormap']
- cmap = plt.get_cmap(colormap)
- color = cmap(np.linspace(0,1,len(specs)))
- else:
- colormap = False
-
- if 'scaling' in params:
- scaling = params['scaling']
- else:
- scaling = False
-
- if 'x_axis' in params:
- x_axis = params['x_axis']
- else:
- x_axis = False
-
- if 'y_axis' in params:
- y_axis = params['y_axis']
- else:
- y_axis = False
- #######
-
- fig = plt.figure(figsize=(6,4))
-
- counter = 0
- for (s, c) in zip(specs, color):
-
- (x_data, x_unit) = s.get_channel(channelx, direction=direction)
- if x_axis:
- x_data = np.clip(x_data, x_axis[0], x_axis[1])
-
- (y_data, y_unit) = s.get_channel(channely, direction=direction)
- if y_axis:
- y_data = np.clip(y_data, y_axis[0], y_axis[1])
-
- if scaling:
- if scaling == 'lin-lin':
- plt.plot(x_data, y_data, color=c, label=s.name)
- elif scaling == "lin-log":
- plt.semilogy(x_data, np.abs(y_data), color=c, label=s.name)
- elif scaling == 'log-lin':
- plt.semilogx(np.abs(x_data), y_data, color=c, label=s.name)
- elif scaling == 'log-log':
- plt.loglog(np.abs(x_data), np.abs(y_data), color=c, label=s.name)
- else:
- plt.plot(x_data, y_data, color=c, label=s.name)
- else:
- plt.plot(x_data,y_data+counter*offset,color = c,label = s.name)
- counter = counter + 1
-
- plt.xlabel('%s (%s)' % (channelx,x_unit))
- plt.ylabel('%s (%s)' % (channely,y_unit))
-
- if print_legend:
- plt.legend()
-
- if show:
- plt.show()
-
- return fig
-
-
-def relative_position(img,spec,**params):
-
- #width = ref.get_param('width')
- #height = ref.get_param('height')
- #[px_x,px_y] = ref.get_param('scan_pixels')
-
- [o_x,o_y] = img.get_param('scan_offset')
- width = img.get_param('width')[0]
- height = img.get_param('height')[0]
- [o_x,o_y] = [o_x*10**9,o_y*10**9]
-
- angle = float(img.get_param('scan_angle'))*-1* np.pi/180
-
-
- x_spec = spec.get_param('x')[0]
- y_spec = spec.get_param('y')[0]
-
- if angle != 0:
- #Transforming to relative coordinates with angle
- x_rel = (x_spec-o_x)*np.cos(angle) + (y_spec-o_y)*np.sin(angle)+width/2
- y_rel = -(x_spec-o_x)*np.sin(angle) + (y_spec-o_y)*np.cos(angle)+height/2
- else:
- x_rel = x_spec-o_x+width/2
- y_rel = y_spec-o_y+height/2
- return [x_rel,y_rel]
-
-
-
-def ref_spec_plotting(ref_file,spec_files,fname_ref,fname_specs,**params):
- """
- Plots sxm reference image with spectra locations and multiple dat spectra
-
- Input:
- ref_file: filename of reference sxm image
- spec_files: list of filenames of dat spectra
- fname_ref: filename of saved reference image
- fname_specs: filename of saved spectra image
-
- Optional input:
- channelx_plot: channel to plot on x-axis of dat spectra (default: V)
- channely_plot: channel to plot on y-axis of dat spectra (default: dIdV)
- offset: offset between spectra (default: 0)
- annotate_spec: annotate spectra with numbers
-
- Output:
- specs_fig: figure of spectra
- """
-
-
- # Load modules
- import os
-
- # Optional input
- if 'channelx_plot' in params:
- channelx_plot = params['channelx_plot']
- else:
- channelx_plot = 'V'
-
- if 'channely_plot' in params:
- channely_plot = params['channely_plot']
- else:
- channely_plot = 'dIdV'
-
- if 'print_legend' not in params:
- params['print_legend'] = True
-
- if 'annotate_spec' in params:
- annotate_spec = params['annotate_spec']
- else:
- annotate_spec = False
-
-
- ## Import
- # Importing reference image
- ref = spm(ref_file)
-
- # Importing spec
- sp = []
- for s in spec_files:
- sp.append(spm(s))
-
- # Defining color scale
- col = pl.cm.rainbow(np.linspace(0,1,len(sp)))
-
- ## Plotting reference image with spec locations
- ref.plot(show_params = True, offset = False, show = False,channel = 'z',close_fig = False);
-
- # plot circle for each location
- for (s,c) in zip(sp,col):
- (x,y) = relative_position(ref,s)
- plt.plot(x,y,'o',color = c)
- if annotate_spec:
- plt.annotate(s.name, (x,y))
-
- plt.xlabel('x (nm)')
- plt.ylabel('y (nm)')
-
- figDir = os.path.abspath(os.path.join(fname_ref, os.pardir))
- if not os.path.exists(figDir):
- os.makedirs(figDir)
-
-
- plt.savefig(fname_ref+'.png', dpi=500)
- plt.savefig(fname_ref+'.svg', dpi=500)
-
- # Plotting specs
- specs_fig = specs_plot(sp,channelx=channelx_plot,channely=channely_plot, direction = 'forward', color = col,**params);
-
- figDir = os.path.abspath(os.path.join(fname_specs, os.pardir))
- if not os.path.exists(figDir):
- os.makedirs(figDir)
-
- specs_fig.savefig(fname_specs+'.png', dpi=500)
- specs_fig.savefig(fname_specs+'.svg', dpi=500)
-
- plt.show()
-
- return specs_fig
-
-
-
-# returns dict list of fitted kpfm parabolas for list of spm objects
-def kpfm(files,**params):
-
- if 'range' in params:
- range = params['range'];
- else:
- range = [0,len(files[0].get_channel('V')[0])-1]
-
- import numpy as np
- #sys.path.append('../')
- #import analyze as an
-
- data = {'V': [], 'df': [], 'V_max': [], 'df_max': [], 'p_fit': [], 'err_p': [], 'V_fit': [], 'df_fit': [], 'err_V_max': [], 'err_df_max': [], 'position': []}
-
- for f in files:
- if f.type == 'spec':
- if any(d['ChannelNickname'] == 'df' for d in f.SignalsList):
-
- data['V'].append(f.get_channel('V')[0])
- data['df'].append(f.get_channel('df')[0])
-
- if any(d['ChannelNickname'] == 'df_bw' for d in f.SignalsList):
-
- if not('df_bw' in data.keys()):
- data['V_bw'] = [];
- data['df_bw'] = [];
-
- else:
- data['V_bw'].append(f.get_channel('V_bw')[0])
- data['df_bw'].append(f.get_channel('df_bw')[0])
-
- x = f.get_param('x')[0]
- y = f.get_param('y')[0]
-
- data['position'].append([x,y])
-
-
- (p_fit,err_p,df_fit,V_max,err_V_max,df_max,err_df_max) = fit_parabola(np.array(data['V'])[:,range[0]:range[1]].tolist(),np.array(data['df'])[:,range[0]:range[1]].tolist(),single_spectrum=False,fitMin=False,fitMax=False)
-
- data['p_fit'] = p_fit;
- data['err_p'] = err_p;
- data['V_fit'] = np.array(data['V'])[:,range[0]:range[1]].tolist();
- data['df_fit'] = df_fit;
- data['V_max'] = V_max;
- data['err_V_max'] = err_V_max;
- data['df_max'] = df_max;
- data['err_df_max'] = err_df_max;
-
- if 'df_bw' in data.keys():
-
- (p_fit_bw,err_p_bw,df_fit_bw,V_max_bw,err_V_max_bw,df_max_bw,err_df_max_bw) = fit_parabola(np.array(data['V_bw'])[:,range[0]:range[1]].tolist(),np.array(data['df_bw'])[:,range[0]:range[1]].tolist(),single_spectrum=False,fitMin=False,fitMax=False)
-
- data['p_fit_bw'] = p_fit_bw;
- data['err_p_bw'] = err_p_bw;
- data['V_fit_bw'] = np.array(data['V_bw'])[:,range[0]:range[1]].tolist()
- data['df_fit_bw'] = df_fit_bw;
- data['V_max_bw'] = V_max_bw;
- data['err_V_max_bw'] = err_V_max_bw;
- data['df_max_bw'] = df_max_bw;
- data['err_df_max_bw'] = err_df_max_bw;
-
- return data
-
-
-
-
-
-##############################################
-# help functions
-##############################################
-
-def fit_parabola(
- bias,
- df,
- single_spectrum=False,
- fitMin=False,
- fitMax=False,
- ):
-
- #import numpy as np
-
- if single_spectrum:
- bias = np.array([bias])
- df = np.array([df])
- p_fit = np.zeros((len(bias), 3))
- df_fit = np.zeros((len(bias), len(bias[0])))
- err_p = np.zeros((len(bias), 3))
- bias_max = np.zeros(len(bias))
- err_bias_max = np.zeros(len(bias))
- df_max = np.zeros(len(bias))
- err_df_max = np.zeros(len(bias))
-
- for i in range(len(bias)):
- if not fitMin and not fitMax:
- (p, cov) = np.polyfit(bias[i], df[i], 2, cov=True)
- elif fitMin and not fitMax:
-
- fit_i = np.where(bias[i] > fitMin[i])[0]
- (p, cov) = np.polyfit(bias[i, fit_i], df[i, fit_i], 2,
- cov=True)
- p_fit[i] = p
- err1 = np.sqrt(abs(cov))
- err_p[i] = np.array([err1[0, 0], err1[1, 1], err1[2, 2]])
-
- df_fit[i] = np.polyval(p, bias[i])
-
- bias_max[i] = -p[1] / (2 * p[0])
-
- # if errors independent
-
- #err_bias_max[i] = abs(bias_max[i]) * np.sqrt((err1[1, 1]
- # / p[1]) ** 2 + (err1[0, 0] / p[0]) ** 2)
- err_bias_max[i] = np.sqrt((err1[1, 1]/ (2*p[0]))** 2 + (err1[0, 0]*p[1] /(2*p[0]**2)) ** 2)
-
- # maximum error in any case (John Tayler Error analysis book)
-
- #err_bias_max[i] = abs(bias_max[i]) * (err1[1, 1] + err1[0, 0])
-
- df_max[i] = np.polyval(p, bias_max[i])
- err_df_max[i] = p[0] * bias_max[i] ** 2 * (err1[0, 0] + 2
- * err_bias_max[i] / abs(bias_max[i])) + p[1] \
- * bias_max[i] * (err1[1, 1] + err_bias_max[i]
- / abs(bias_max[i])) + p[2] * err1[2, 2]
- return (
- p_fit,
- err_p,
- df_fit,
- bias_max,
- err_bias_max,
- df_max,
- err_df_max,
- )
-
-# this function returns a rgb color code according to standard matlab colors
-def matlab_color(num):
- if num > 6:
- num = np.mod(num,7)
-
- colors = [[0,0.4470,0.7410],
- [0.8500,0.3250,0.0980],
- [0.9290,0.6940,0.1250],
- [0.4940,0.1840,0.5560],
- [0.4660,0.6740,0.1880],
- [0.3010,0.7450,0.9330],
- [0.6350,0.0780,0.1840]]
-
- return colors[np.round(num)]
-