Skip to content
Snippets Groups Projects
Commit 4ee77e17 authored by cramakri's avatar cramakri
Browse files

LMS-2472 Refactored the image generation script 

SVN: 22733
parent 0473da42
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
test-data/screening/source/python/generate-test-plate.py
+ 5
− 150
View file @ 4ee77e17
#!/usr/bin/env python #!/usr/bin/env python
""" """
A module for generating test plates and overlays for the screening version of openBIS Generate a plate.
""" """
import canvas import imagegen
import math
import os import os
import shutil 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): def overlayTests(sampleCode):
rootDir = "targets/generated-images" rootDir = "targets/generated-images"
...@@ -182,12 +37,12 @@ def recreateDir(dir): ...@@ -182,12 +37,12 @@ def recreateDir(dir):
os.mkdir(dir) os.mkdir(dir)
recreateDir("PLATONIC") recreateDir("PLATONIC")
config = PlateGeneratorConfig() config = imagegen.PlateGeneratorConfig()
# Alternative Configurations # Alternative Configurations
#config.time_points = [ 5, 10, 15 ] #config.time_points = [ 5, 10, 15 ]
#config.depth_points = [ 3, 6, 9 ] #config.depth_points = [ 3, 6, 9 ]
#config.is_split = True #config.is_split = True
generator = PlateGenerator(config) generator = imagegen.PlateGenerator(config)
generator.generate_raw_images("PLATONIC") generator.generate_raw_images("PLATONIC")
\ No newline at end of file
test-data/screening/source/python/imagegen.py 0 → 100644
+ 167
− 0
View file @ 4ee77e17
#!/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()
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment