From 4ee77e173dbea03410764c81c8f3a3c26b403d6f Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 31 Aug 2011 08:44:34 +0000
Subject: [PATCH] LMS-2472 Refactored the image generation script
SVN: 22733
---
.../source/python/generate-test-plate.py | 155 +---------------
test-data/screening/source/python/imagegen.py | 167 ++++++++++++++++++
2 files changed, 172 insertions(+), 150 deletions(-)
create mode 100644 test-data/screening/source/python/imagegen.py
diff --git a/test-data/screening/source/python/generate-test-plate.py b/test-data/screening/source/python/generate-test-plate.py
index 6dabff06235..ab1e5457ff4 100755
--- a/test-data/screening/source/python/generate-test-plate.py
+++ b/test-data/screening/source/python/generate-test-plate.py
@@ -1,157 +1,12 @@
#!/usr/bin/env python
"""
-A module for generating test plates and overlays for the screening version of openBIS
+Generate a plate.
"""
-import canvas
-import math
+import imagegen
import os
import shutil
-import string
-
-def generate_tile_description(tile, time = None, depth = None):
- """
- Generate a description for the combination of well, tile, channel
- and, optionaly, depth and/or time
- """
-
- desc = "s"+ str(tile)
- if depth is not None:
- desc = desc + "_z" + str(depth)
- if time is not None:
- desc = desc + "_t" + str(time)
- return desc
-
-def generate_file_name(well, channel, desc):
- """
- Generate a name for a file using the description and channel
- """
-
- return "bPLATE_w" + well + "_" + desc + "_c" + channel + ".png"
-
-def drawRect(canvas, r, g, b, start, isUnfilled = 0):
- canvas.draw_inset_rect(r, g, b, start, isUnfilled)
-
-def drawText(canvas, x, y, text):
- canvas.draw_text(x, y, text)
-
-def calcTile(coords):
- x,y = coords
- return (y-1)*3+x
-
-class ImageGeneratorConfig:
- """
- Represents the configuration options for generating images
- """
- def __init__(self):
- self.number_of_tiles = 9
- self.image_size = 512
- self.is_split = False
- # Use an array with None for not time points / depth points
- self.time_points = [ None ]
- self.depth_points = [ None ]
- self.tile_description_generator = generate_tile_description
- self.file_name_generator = generate_file_name
-
-class PlateGeneratorConfig(ImageGeneratorConfig):
- """
- Represents the configuration options for generating plates
- """
- def __init__(self):
- ImageGeneratorConfig.__init__(self)
- self.rows = 8
- self.cols = 12
-
-class WellGenerator:
- """
- A class that generates raw images or overlays for a well. Used by the PlateGenerator and ImageGenerator.
- """
-
- def __init__(self, config, well, directory):
- """Constructor that takes the config and the well we are generating images for."""
- self.config = config
- self.well = well
- self.directory = directory
-
- def generate_raw_images(self):
- for tile in range(1, self.config.number_of_tiles + 1):
- for time in self.config.time_points:
- for depth in self.config.depth_points:
- desc = self.config.tile_description_generator(tile, time, depth)
- if self.config.is_split:
- file_name = self.config.file_name_generator(self.well, "RED", desc)
- self._generate_tile(file_name, desc, 1, 0, 0)
-
- file_name = self.config.file_name_generator(self.well, "GREEN", desc)
- self._generate_tile(file_name, desc, 0, 1, 0)
-
- file_name = self.config.file_name_generator(self.well, "BLUE", desc)
- self._generate_tile(file_name, desc, 0, 0, 1)
- else:
- file_name = self.config.file_name_generator(self.well, "RGB", desc)
- self._generate_tile(file_name, desc, 1, 1, 1)
-
- def _generate_tile(self, filename, tile_desc, r, g, b):
- tile_canvas = canvas.TileCanvas(self.config.image_size, self.config.image_size)
- drawRect(tile_canvas, 0, 0, 0, 0) # fill with black
-
- if self.config.is_split:
- # if split, we want to draw white instead of the specified color, since
- # the channel assignment will happen in openBIS, not here
- if r:
- drawRect(tile_canvas, 1, 1, 1, 20) # red
- if g:
- drawRect(tile_canvas, 1, 1, 1, 70) # green
- if b:
- drawRect(tile_canvas, 1, 1, 1, 120) # blue
- else:
- drawRect(tile_canvas, 1, 0, 0, 20) # red
- drawRect(tile_canvas, 0, 1, 0, 70) # green
- drawRect(tile_canvas, 0, 0, 1, 120) # blue
-
- # text annotation
- drawText(tile_canvas, 5, self.config.image_size / 2, tile_desc)
- drawText(tile_canvas, 5, 5, self.well)
-
- # Write the bitmap to disk in PNG format
- tile_canvas.write_png_file(self.directory + "/" + filename)
-
- def drawMatrix(self, coordsList, dir, channel, isOverlay):
- nonemptyTiles = set([ calcTile(coords) for coords in coordsList ])
- for tile in range(1, 10):
- imageCanvas = canvas.TileCanvas(self.config.image_size, self.config.image_size)
- if tile in nonemptyTiles:
- if not isOverlay:
- drawRect(imageCanvas, 0, 0, 0, 0)
- drawRect(imageCanvas, 0.5, 0.5, 0.5, 70, isUnfilled = 0)
- elif isOverlay == 1:
- drawRect(imageCanvas, 1, 1, 1, 30, isUnfilled = 1)
- else:
- drawText(imageCanvas, size/2, size/2, "X")
- destFile = dir + "/c"+channel + "_s" + str(tile) +".png"
- imageCanvas.write_png_file(destFile)
-
-
-class PlateGenerator:
- """
- A class that generates raw images or overlays for a plate.
-
- To use, instantiate it with a PlateGeneratorConfig that describes its properties, then
- call generate_raw_images or generate_overlays
- """
-
- def __init__(self, config):
- """Constructor that takes the configuration for the plate"""
- self.config = config
-
- def generate_raw_images(self, directory):
- for row in range(0, self.config.rows):
- for col in range(1, self.config.cols + 1):
- well = string.letters[26 + row] + str(col)
- well_generator = WellGenerator(self.config, well, directory)
- well_generator.generate_raw_images()
-
def overlayTests(sampleCode):
rootDir = "targets/generated-images"
@@ -182,12 +37,12 @@ def recreateDir(dir):
os.mkdir(dir)
recreateDir("PLATONIC")
-config = PlateGeneratorConfig()
+config = imagegen.PlateGeneratorConfig()
# Alternative Configurations
#config.time_points = [ 5, 10, 15 ]
#config.depth_points = [ 3, 6, 9 ]
#config.is_split = True
-generator = PlateGenerator(config)
-generator.generate_raw_images("PLATONIC")
\ No newline at end of file
+generator = imagegen.PlateGenerator(config)
+generator.generate_raw_images("PLATONIC")
diff --git a/test-data/screening/source/python/imagegen.py b/test-data/screening/source/python/imagegen.py
new file mode 100644
index 00000000000..5e9f95ab089
--- /dev/null
+++ b/test-data/screening/source/python/imagegen.py
@@ -0,0 +1,167 @@
+#!/usr/bin/env python
+
+"""
+A module with classes and functions for generating test images, plates, and overlays for the screening version of openBIS.
+"""
+
+import canvas
+import string
+
+def generate_tile_description(tile, time = None, depth = None):
+ """
+ Generate a description for the combination of well, tile, channel
+ and, optionaly, depth and/or time
+ """
+
+ desc = "s"+ str(tile)
+ if depth is not None:
+ desc = desc + "_z" + str(depth)
+ if time is not None:
+ desc = desc + "_t" + str(time)
+ return desc
+
+def generate_file_name(well, channel, desc):
+ """
+ Generate a name for a file using the description and channel
+ """
+
+ return "bPLATE_w" + well + "_" + desc + "_c" + channel + ".png"
+
+def drawRect(canvas, r, g, b, start, isUnfilled = 0):
+ canvas.draw_inset_rect(r, g, b, start, isUnfilled)
+
+def drawText(canvas, x, y, text):
+ canvas.draw_text(x, y, text)
+
+def calcTile(coords):
+ x,y = coords
+ return (y-1)*3+x
+
+class ImageGeneratorConfig:
+ """
+ Represents the configuration options for generating images
+ """
+ def __init__(self):
+ self.number_of_tiles = 9
+ self.image_size = 512
+ self.is_split = False
+ # Use an array with None for not time points / depth points
+ self.time_points = [ None ]
+ self.depth_points = [ None ]
+ self.tile_description_generator = generate_tile_description
+ self.file_name_generator = generate_file_name
+
+class PlateGeneratorConfig(ImageGeneratorConfig):
+ """
+ Represents the configuration options for generating plates
+ """
+ def __init__(self):
+ ImageGeneratorConfig.__init__(self)
+ self.rows = 8
+ self.cols = 12
+
+class WellGenerator:
+ """
+ A class that generates raw images or overlays for a well. Used by the PlateGenerator and ImageGenerator.
+ """
+
+ def __init__(self, config, well, directory):
+ """Constructor that takes the config and the well we are generating images for."""
+ self.config = config
+ self.well = well
+ self.directory = directory
+
+ def generate_raw_images(self):
+ for tile in range(1, self.config.number_of_tiles + 1):
+ for time in self.config.time_points:
+ for depth in self.config.depth_points:
+ desc = self.config.tile_description_generator(tile, time, depth)
+ if self.config.is_split:
+ file_name = self.config.file_name_generator(self.well, "RED", desc)
+ self._generate_tile(file_name, desc, 1, 0, 0)
+
+ file_name = self.config.file_name_generator(self.well, "GREEN", desc)
+ self._generate_tile(file_name, desc, 0, 1, 0)
+
+ file_name = self.config.file_name_generator(self.well, "BLUE", desc)
+ self._generate_tile(file_name, desc, 0, 0, 1)
+ else:
+ file_name = self.config.file_name_generator(self.well, "RGB", desc)
+ self._generate_tile(file_name, desc, 1, 1, 1)
+
+ def _generate_tile(self, filename, tile_desc, r, g, b):
+ tile_canvas = canvas.TileCanvas(self.config.image_size, self.config.image_size)
+ drawRect(tile_canvas, 0, 0, 0, 0) # fill with black
+
+ if self.config.is_split:
+ # if split, we want to draw white instead of the specified color, since
+ # the channel assignment will happen in openBIS, not here
+ if r:
+ drawRect(tile_canvas, 1, 1, 1, 20) # red
+ if g:
+ drawRect(tile_canvas, 1, 1, 1, 70) # green
+ if b:
+ drawRect(tile_canvas, 1, 1, 1, 120) # blue
+ else:
+ drawRect(tile_canvas, 1, 0, 0, 20) # red
+ drawRect(tile_canvas, 0, 1, 0, 70) # green
+ drawRect(tile_canvas, 0, 0, 1, 120) # blue
+
+ # text annotation
+ drawText(tile_canvas, 5, self.config.image_size / 2, tile_desc)
+ drawText(tile_canvas, 5, 5, self.well)
+
+ # Write the bitmap to disk in PNG format
+ tile_canvas.write_png_file(self.directory + "/" + filename)
+
+ def drawMatrix(self, coordsList, dir, channel, isOverlay):
+ nonemptyTiles = set([ calcTile(coords) for coords in coordsList ])
+ for tile in range(1, 10):
+ imageCanvas = canvas.TileCanvas(self.config.image_size, self.config.image_size)
+ if tile in nonemptyTiles:
+ if not isOverlay:
+ drawRect(imageCanvas, 0, 0, 0, 0)
+ drawRect(imageCanvas, 0.5, 0.5, 0.5, 70, isUnfilled = 0)
+ elif isOverlay == 1:
+ drawRect(imageCanvas, 1, 1, 1, 30, isUnfilled = 1)
+ else:
+ drawText(imageCanvas, size/2, size/2, "X")
+ destFile = dir + "/c"+channel + "_s" + str(tile) +".png"
+ imageCanvas.write_png_file(destFile)
+
+
+class PlateGenerator:
+ """
+ A class that generates raw images or overlays for a plate. Similar
+ to GenericImageGenerator, but with plates added.
+
+ To use, instantiate it with a PlateGeneratorConfig that describes its properties, then
+ call generate_raw_images or generate_overlays
+ """
+
+ def __init__(self, config):
+ """Constructor that takes the configuration for the plate"""
+ self.config = config
+
+ def generate_raw_images(self, directory):
+ for row in range(0, self.config.rows):
+ for col in range(1, self.config.cols + 1):
+ well = string.letters[26 + row] + str(col)
+ well_generator = WellGenerator(self.config, well, directory)
+ well_generator.generate_raw_images()
+
+class GenericImageGenerator:
+ """
+ A class that generates raw images or overlays simulating images from a microscope. Similar to PlateGenerator, except without the plates.
+
+ To use, instantiate it with a ImageGeneratorConfig that describes its properties, then
+ call generate_raw_images or generate_overlays
+ """
+
+ def __init__(self, config):
+ """Constructor that takes the configuration for the plate"""
+ self.config = config
+
+ def generate_raw_images(self, directory):
+ well_generator = WellGenerator(self.config, "", directory)
+ well_generator.generate_raw_images()
--
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