# HG changeset patch
# User bgruening
# Date 1587029619 14400
# Node ID 2005f80580367816eb14eae06e6fd7947aafe4c6
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
diff -r 000000000000 -r 2005f8058036 cp_common_functions.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cp_common_functions.py Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,61 @@
+INDENTATION = " "
+LINE_NUM_MODULES = 4
+
+def get_json_value(json_input, keys_path):
+ """Returns the value specified in keys_path (using dot notation) or an empty string if the key doesn't exist"""
+ if not isinstance(json_input, dict):
+ return ""
+ keys = keys_path.split(".")
+ try:
+ value = json_input[keys[0]]
+ for key in keys[1:]:
+ value = value[key]
+ return value
+ except KeyError:
+ return ""
+
+
+def concat_conditional(a, b):
+ if a == "" or b == "":
+ return ""
+ else:
+ return f"{a}_{b}"
+
+
+def get_total_number_of_modules(pipeline_lines):
+ """Gets the number of modules from the header of the previous pipeline"""
+ number_of_modules = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[1]
+ return int(number_of_modules)
+
+
+def get_pipeline_lines(input_pipeline):
+ """Returns a list with the lines in the .cppipe file"""
+ with open(input_pipeline) as f:
+ lines = f.readlines()
+ return lines
+
+
+def update_module_count(pipeline_lines, count):
+ """Updates the number of modules in the .cppipe header"""
+ module_count_entry = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[0]
+ pipeline_lines[4] = f"{module_count_entry}:{count}\n"
+ return pipeline_lines
+
+
+def write_pipeline(filename, lines_pipeline):
+ """Writes the lines composing the pipeline into a file"""
+ with open(filename, "w") as f:
+ f.writelines(lines_pipeline)
+
+
+def build_header(module_name, module_number):
+ """Creates the first line of a module given the name and module number"""
+ result = "|".join([f"{module_name}:[module_num:{module_number}",
+ "svn_version:\\'Unknown\\'",
+ "variable_revision_number:4",
+ "show_window:False",
+ "notes:\\x5B\\x5D",
+ "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+ "enabled:True",
+ "wants_pause:False]\n"])
+ return result
diff -r 000000000000 -r 2005f8058036 image_math.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/image_math.py Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,129 @@
+#!/usr/bin/env python
+
+import json
+import sys
+import os
+import argparse
+from cp_common_functions import *
+
+MODULE_NAME = "ImageMath"
+OUTPUT_FILENAME = "output.cppipe"
+
+operator_map = {
+ "add": "Add",
+ "subtract": "Subtract",
+ "multiply": "Multiply",
+ "divide": "Divide",
+ "average": "Average",
+ "minimum": "Minimum",
+ "maximum": "Maximum",
+ "invert": "Invert",
+ "log_2": "Log transform (base 2)",
+ "log_legacy": "Log transform (legacy)",
+ "and": "And",
+ "or": "Or",
+ "not": "Not",
+ "equals": "Equals"
+}
+
+
+def build_main_block(input_params):
+ """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
+ operation = operator_map[get_json_value(
+ input_params, 'operation.operation')]
+ result = INDENTATION.join([f"{INDENTATION}Operation:{operation}\n",
+ f"Raise the power of the result by:{get_json_value(input_params,'operation.op_results.raise_the_power_of_the_result_by')}\n",
+ f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n",
+ f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n",
+ f"Set values less than 0 equal to 0?:{get_json_value(input_params,'operation.op_results.set_values_less_than_0_equal_to_0')}\n",
+ f"Set values greater than 1 equal to 1?:{get_json_value(input_params,'operation.op_results.set_values_greater_than_1_equal_to_1')}\n",
+ f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n",
+ f"Name the output image:{get_json_value(input_params,'name_output_image')}"
+ ])
+ return result
+
+
+def build_variable_block(inputs_galaxy):
+ result = ""
+ first_image_block = build_first_image_block(
+ get_json_value(inputs_galaxy, 'operation.first_image'))
+ result += f"\n{first_image_block}"
+ second_image_block = build_second_image_block(
+ get_json_value(inputs_galaxy, 'operation.second_image'))
+ result += f"\n{second_image_block}"
+ return result
+
+
+def build_first_image_block(input_params):
+ """Creates the block of parameters for the first operator in operations"""
+
+ value_select = get_json_value(
+ input_params, 'image_or_measurement_first.image_or_measurement_first')
+ image_name = get_json_value(
+ input_params, 'image_or_measurement_first.select_the_first_image')
+ value_multiply = get_json_value(
+ input_params, 'multiply_the_first_image_by')
+ category = get_json_value(
+ input_params, 'image_or_measurement_first.category_first.category_first')
+ measurement = get_json_value(
+ input_params, 'image_or_measurement_first.category_first.measurement_first')
+
+ result = INDENTATION.join(
+ [f"{INDENTATION}Image or measurement?:{value_select}\n",
+ f"Select the first image:{image_name}\n",
+ f"Multiply the first image by:{value_multiply}\n",
+ f"Measurement:{concat_conditional(category, measurement)}"
+ ])
+ return result
+
+
+def build_second_image_block(input_params):
+ """Creates the block of parameters for the second operator in binary operations"""
+
+ value_select = get_json_value(
+ input_params, 'image_or_measurement_second.image_or_measurement_second')
+ image_name = get_json_value(
+ input_params, 'image_or_measurement_second.select_the_second_image')
+ value_multiply = get_json_value(
+ input_params, 'multiply_the_second_image_by')
+ category = get_json_value(
+ input_params, 'image_or_measurement_second.category_second.category_second')
+ measurement = get_json_value(
+ input_params, 'image_or_measurement_second.category_second.measurement_second')
+
+ result = INDENTATION.join(
+ [f"{INDENTATION}Image or measurement?:{value_select}\n",
+ f"Select the second image:{image_name}\n",
+ f"Multiply the second image by:{value_multiply}\n",
+ f"Measurement:{concat_conditional(category, measurement)}"
+ ])
+ return result
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser()
+ parser.add_argument(
+ '-p', '--pipeline',
+ help='CellProfiler pipeline'
+ )
+ parser.add_argument(
+ '-i', '--inputs',
+ help='JSON inputs from Galaxy'
+ )
+ args = parser.parse_args()
+
+ pipeline_lines = get_pipeline_lines(args.pipeline)
+ inputs_galaxy = json.load(open(args.inputs, "r"))
+
+ current_module_num = get_total_number_of_modules(pipeline_lines)
+ current_module_num += 1
+ pipeline_lines = update_module_count(pipeline_lines, current_module_num)
+
+ header_block = build_header(MODULE_NAME, current_module_num)
+ main_block = build_main_block(inputs_galaxy)
+ variable_block = build_variable_block(inputs_galaxy)
+
+ module_pipeline = f"\n{header_block}{main_block}{variable_block}\n"
+ pipeline_lines.append(module_pipeline)
+
+ write_pipeline(OUTPUT_FILENAME, pipeline_lines)
diff -r 000000000000 -r 2005f8058036 image_math.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/image_math.xml Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,296 @@
+
+ perform simple mathematical operations on images
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 2005f8058036 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,105 @@
+
+ 3.1.9
+ 3.7
+ jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps
+ " "
+
+
+ .. class:: infomark
+
+ **Input**
+
+ Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
+
+ .. class:: infomark
+
+ **Output**
+
+ The input CellProfiler pipeline file *(.cppipe)* in addition to the settings of this module.
+
+ .. class:: warningmark
+
+ **IMPORTANT**
+
+ The first tool in a CellProfiler workflow has to be **Starting modules** and the last one **CellProfiler**. You can also execute the entire pipeline with the final CellProfiler tool, in which you feed in the images you want to process as well.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ cellprofiler
+
+
+
+
+
+
+ python
+
+
+
+
+
+
+
+ @article{McQuin_2018,
+ title = {CellProfiler 3.0: Next-generation image processing for biology},
+ author = {McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE},
+ year = {2018},
+ volume = {16(7):e2005970},
+ DOI = {10.1371/journal.pbio.2005970},
+ journal = {PLoS Biol.},
+ url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970},
+ }
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ^[A-Za-z0-9 _-]*$
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)
+
+ Input: existing pipeline file
+
+ Output: new pipeline file
+
+ Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.
+
+
+
+
diff -r 000000000000 -r 2005f8058036 test-data/ExampleHuman.cppipe
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ExampleHuman.cppipe Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,246 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:300
+GitHash:
+ModuleCount:14
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\x5B\\\\\\\\\\\\\\\\/\x5D\\\\\\\\.")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:No
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:^(?P.*)_(?P\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P\x5B0-9\x5D)_w(?P\x5B0-9\x5D)
+ Regular expression to extract from folder name:(?P\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:\x5B\x5D
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'DNA\x3A DNA stained with DAPI\', \'PH3\x3A An antibody for phosphorylated histone H3 correlated with mitosis\', \'cellbody\x3A \'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:\x5B\x5D
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:3
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does contain "d0.tif")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Maximum intensity:255.0
+ Select the rule criteria:and (file does contain "d1.tif")
+ Name to assign these images:PH3
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Maximum intensity:255.0
+ Select the rule criteria:and (file does contain "d2.tif")
+ Name to assign these images:cellbody
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:No
+ grouping metadata count:1
+ Metadata category:None
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input image:DNA
+ Name the primary objects to be identified:Nuclei
+ Typical diameter of objects, in pixel units (Min,Max):8,80
+ Discard objects outside the diameter range?:Yes
+ Discard objects touching the border of the image?:Yes
+ Method to distinguish clumped objects:Intensity
+ Method to draw dividing lines between clumped objects:Intensity
+ Size of smoothing filter:10
+ Suppress local maxima that are closer than this minimum allowed distance:7.0
+ Speed up by using lower-resolution image to find local maxima?:Yes
+ Fill holes in identified objects?:After declumping only
+ Automatically calculate size of smoothing filter for declumping?:Yes
+ Automatically calculate minimum allowed distance between local maxima?:Yes
+ Handling of objects if excessive number of objects identified:Continue
+ Maximum number of objects:500
+ Use advanced settings?:No
+ Threshold setting version:10
+ Threshold strategy:Global
+ Thresholding method:Minimum cross entropy
+ Threshold smoothing scale:1.3488
+ Threshold correction factor:1.0
+ Lower and upper bounds on threshold:0.0,1.0
+ Manual threshold:0.0
+ Select the measurement to threshold with:None
+ Two-class or three-class thresholding?:Two classes
+ Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+ Size of adaptive window:50
+ Lower outlier fraction:0.05
+ Upper outlier fraction:0.05
+ Averaging method:Mean
+ Variance method:Standard deviation
+ # of deviations:2.0
+ Thresholding method:Otsu
+
+IdentifyPrimaryObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input image:PH3
+ Name the primary objects to be identified:PH3
+ Typical diameter of objects, in pixel units (Min,Max):8,80
+ Discard objects outside the diameter range?:Yes
+ Discard objects touching the border of the image?:Yes
+ Method to distinguish clumped objects:Intensity
+ Method to draw dividing lines between clumped objects:Intensity
+ Size of smoothing filter:10
+ Suppress local maxima that are closer than this minimum allowed distance:7.0
+ Speed up by using lower-resolution image to find local maxima?:Yes
+ Fill holes in identified objects?:After declumping only
+ Automatically calculate size of smoothing filter for declumping?:Yes
+ Automatically calculate minimum allowed distance between local maxima?:Yes
+ Handling of objects if excessive number of objects identified:Continue
+ Maximum number of objects:500
+ Use advanced settings?:No
+ Threshold setting version:10
+ Threshold strategy:Global
+ Thresholding method:Minimum cross entropy
+ Threshold smoothing scale:1.3488
+ Threshold correction factor:1.0
+ Lower and upper bounds on threshold:0.0,1.0
+ Manual threshold:0.0
+ Select the measurement to threshold with:None
+ Two-class or three-class thresholding?:Two classes
+ Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+ Size of adaptive window:50
+ Lower outlier fraction:0.05
+ Upper outlier fraction:0.05
+ Averaging method:Mean
+ Variance method:Standard deviation
+ # of deviations:2.0
+ Thresholding method:Otsu
+
+RelateObjects:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Parent objects:Nuclei
+ Child objects:PH3
+ Calculate child-parent distances?:None
+ Calculate per-parent means for all child measurements?:No
+ Calculate distances to other parents?:No
+ Parent name:None
+
+IdentifySecondaryObjects:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:10|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input objects:Nuclei
+ Name the objects to be identified:Cells
+ Select the method to identify the secondary objects:Propagation
+ Select the input image:cellbody
+ Number of pixels by which to expand the primary objects:10
+ Regularization factor:0.05
+ Discard secondary objects touching the border of the image?:No
+ Discard the associated primary objects?:No
+ Name the new primary objects:FilteredNuclei
+ Fill holes in identified objects?:Yes
+ Threshold setting version:10
+ Threshold strategy:Global
+ Thresholding method:Otsu
+ Threshold smoothing scale:0.0
+ Threshold correction factor:1.0
+ Lower and upper bounds on threshold:0.0,1.0
+ Manual threshold:0.0
+ Select the measurement to threshold with:None
+ Two-class or three-class thresholding?:Three classes
+ Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+ Size of adaptive window:50
+ Lower outlier fraction:0.05
+ Upper outlier fraction:0.05
+ Averaging method:Mean
+ Variance method:Standard deviation
+ # of deviations:2.0
+ Thresholding method:Otsu
+
+IdentifyTertiaryObjects:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the larger identified objects:Cells
+ Select the smaller identified objects:Nuclei
+ Name the tertiary objects to be identified:Cytoplasm
+ Shrink smaller object prior to subtraction?:Yes
+
+MeasureObjectIntensity:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Hidden:2
+ Select an image to measure:DNA
+ Select an image to measure:PH3
+ Select objects to measure:Nuclei
+ Select objects to measure:Cells
+ Select objects to measure:Cytoplasm
+
+MeasureObjectSizeShape:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select objects to measure:Nuclei
+ Select objects to measure:Cells
+ Select objects to measure:Cytoplasm
+ Calculate the Zernike features?:Yes
+
+OverlayOutlines:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Display outlines on a blank image?:No
+ Select image on which to display outlines:DNA
+ Name the output image:OrigOverlay
+ Outline display mode:Color
+ Select method to determine brightness of outlines:Max of image
+ How to outline:Thick
+ Select outline color:#0080FF
+ Select objects to display:Cells
+ Select outline color:blue
+ Select objects to display:Nuclei
+ Select outline color:yellow
+ Select objects to display:PH3
+
+SaveImages:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the type of image to save:Image
+ Select the image to save:OrigOverlay
+ Select method for constructing file names:From image filename
+ Select image name for file prefix:DNA
+ Enter single file name:OrigBlue
+ Number of digits:4
+ Append a suffix to the image file name?:Yes
+ Text to append to the image name:_Overlay
+ Saved file format:png
+ Output file location:Default Output Folder\x7C
+ Image bit depth:8-bit integer
+ Overwrite existing files without warning?:Yes
+ When to save:Every cycle
+ Record the file and path information to the saved image?:Yes
+ Create subfolders in the output folder?:No
+ Base image folder:Elsewhere...\x7C
+
+ExportToSpreadsheet:[module_num:14|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the column delimiter:Comma (",")
+ Add image metadata columns to your object data file?:No
+ Select the measurements to export:No
+ Calculate the per-image mean values for object measurements?:No
+ Calculate the per-image median values for object measurements?:No
+ Calculate the per-image standard deviation values for object measurements?:No
+ Output file location:Default Output Folder\x7C
+ Create a GenePattern GCT file?:No
+ Select source of sample row name:Metadata
+ Select the image to use as the identifier:None
+ Select the metadata to use as the identifier:None
+ Export all measurement types?:Yes
+ Press button to select measurements:
+ Representation of Nan/Inf:NaN
+ Add a prefix to file names?:No
+ Filename prefix:MyExpt_
+ Overwrite existing files without warning?:Yes
+ Data to export:Do not use
+ Combine these object measurements with those of the previous object?:No
+ File name:DATA.csv
+ Use the object name for the file name?:Yes
diff -r 000000000000 -r 2005f8058036 test-data/common.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,53 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
diff -r 000000000000 -r 2005f8058036 test-data/common_image_math.cppipe
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common_image_math.cppipe Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,94 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:6
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input image:DNA
+ Name the primary objects to be identified:Nucleus
+ Typical diameter of objects, in pixel units (Min,Max):15,200
+ Discard objects outside the diameter range?:Yes
+ Discard objects touching the border of the image?:Yes
+ Method to distinguish clumped objects:Intensity
+ Method to draw dividing lines between clumped objects:Intensity
+ Size of smoothing filter:10
+ Suppress local maxima that are closer than this minimum allowed distance:7.0
+ Speed up by using lower-resolution image to find local maxima?:Yes
+ Fill holes in identified objects?:After both thresholding and declumping
+ Automatically calculate size of smoothing filter for declumping?:Yes
+ Automatically calculate minimum allowed distance between local maxima?:Yes
+ Handling of objects if excessive number of objects identified:Continue
+ Maximum number of objects:500
+ Use advanced settings?:No
+ Threshold setting version:10
+ Threshold strategy:Global
+ Thresholding method:Minimum cross entropy
+ Threshold smoothing scale:1.3488
+ Threshold correction factor:1.0
+ Lower and upper bounds on threshold:0.0,1.0
+ Manual threshold:0.0
+ Select the measurement to threshold with:None
+ Two-class or three-class thresholding?:Two classes
+ Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+ Size of adaptive window:50
+ Lower outlier fraction:0.05
+ Upper outlier fraction:0.05
+ Averaging method:Mean
+ Variance method:Standard deviation
+ # of deviations:2.0
+ Thresholding method:Otsu
+
+ConvertObjectsToImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input objects:Nucleus
+ Name the output image:CellImage
+ Select the color format:Binary (black & white)
+ Select the colormap:Default
diff -r 000000000000 -r 2005f8058036 test-data/convert_objects_to_image.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/convert_objects_to_image.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,59 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+ConvertObjectsToImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input objects:Nuclei
+ Name the output image:MaskNuclei
+ Select the color format:Binary (black & white)
+ Select the colormap:Default
diff -r 000000000000 -r 2005f8058036 test-data/display_data_on_image.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/display_data_on_image.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,70 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+DisplayDataOnImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Add nuclei id as label\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Display object or image measurements?:Object
+ Select the input objects:Nuclei
+ Measurement to display:Number_Object_Number
+ Select the image on which to display the measurements:DNA
+ Text color:#ff0000
+ Name the output image that has the measurements displayed:ImageDisplay
+ Font size (points):11
+ Number of decimals:0
+ Image elements to save:Image
+ Annotation offset (in pixels):0
+ Display mode:Text
+ Color map:Default
+ Display background image?:Yes
+ Color map scale:Use this image's measurement range
+ Color map range:0.0,1.0
diff -r 000000000000 -r 2005f8058036 test-data/enhance_or_suppress_features.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/enhance_or_suppress_features.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,66 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+EnhanceOrSuppressFeatures:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Identify nucleoli\', \'PARAMS\x3A Range of hole sizes'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input image:DNA
+ Name the output image:DNAdarkholes
+ Select the operation:Enhance
+ Feature size:10
+ Feature type:Dark holes
+ Range of hole sizes:1,15
+ Smoothing scale:2.0
+ Shear angle:0.0
+ Decay:0.95
+ Enhancement method:Tubeness
+ Speed and accuracy:Fast
diff -r 000000000000 -r 2005f8058036 test-data/export_to_spreadsheet.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the column delimiter:Tab
+ Add image metadata columns to your object data file?:Yes
+ Select the measurements to export:No
+ Calculate the per-image mean values for object measurements?:Yes
+ Calculate the per-image median values for object measurements?:Yes
+ Calculate the per-image standard deviation values for object measurements?:Yes
+ Output file location:Default Output Folder\x7C
+ Create a GenePattern GCT file?:No
+ Select source of sample row name:Metadata
+ Select the image to use as the identifier:None
+ Select the metadata to use as the identifier:None
+ Export all measurement types?:Yes
+ Press button to select measurements:
+ Representation of Nan/Inf:NaN
+ Add a prefix to file names?:No
+ Filename prefix:MyPrefix_
+ Overwrite existing files without warning?:Yes
+ Data to export:Do not use
+ Combine these object measurements with those of the previous object?:No
+ File name:DATA.csv
+ Use the object name for the file name?:Yes
diff -r 000000000000 -r 2005f8058036 test-data/gray_to_color.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gray_to_color.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,75 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+GrayToColor:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Combine masks nuclei + nucleoli with colors\'\x5D|batch_state:array(\x5B], dtype=uint8)|enabled:True|wants_pause:False]
+ Select a color scheme:RGB
+ Select the image to be colored red:MaskNucleoli
+ Select the image to be colored green:Leave this black
+ Select the image to be colored blue:MaskNuclei
+ Name the output image:CombinedMask
+ Relative weight for the red image:0.8
+ Relative weight for the green image:1.0
+ Relative weight for the blue image:0.5
+ Select the image to be colored cyan:Leave this black
+ Select the image to be colored magenta:Leave this black
+ Select the image to be colored yellow:Leave this black
+ Select the image that determines brightness:Leave this black
+ Relative weight for the cyan image:1.0
+ Relative weight for the magenta image:1.0
+ Relative weight for the yellow image:1.0
+ Relative weight for the brightness image:1.0
+ Hidden:1
+ Image name:None
+ Color:#FF0000
+ Weight:1.0
diff -r 000000000000 -r 2005f8058036 test-data/identify_primary_objects.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input image:DNA
+ Name the primary objects to be identified:Nuclei
+ Typical diameter of objects, in pixel units (Min,Max):15,200
+ Discard objects outside the diameter range?:Yes
+ Discard objects touching the border of the image?:Yes
+ Method to distinguish clumped objects:Shape
+ Method to draw dividing lines between clumped objects:Shape
+ Size of smoothing filter:0
+ Suppress local maxima that are closer than this minimum allowed distance:7
+ Speed up by using lower-resolution image to find local maxima?:Yes
+ Fill holes in identified objects?:After both thresholding and declumping
+ Automatically calculate size of smoothing filter for declumping?:Yes
+ Automatically calculate minimum allowed distance between local maxima?:Yes
+ Handling of objects if excessive number of objects identified:Continue
+ Maximum number of objects:500
+ Use advanced settings?:Yes
+ Threshold settings version:10
+ Threshold strategy:Global
+ Thresholding method:Otsu
+ Threshold smoothing scale:1.3488
+ Threshold correction factor:0.9
+ Lower and upper bounds on threshold:0.0,1.0
+ Manual threshold:0
+ Select the measurement to threshold with:None
+ Two-class or three-class thresholding?:Two classes
+ Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+ Size of adaptive window:500
+ Lower outlier fraction:0.05
+ Upper outlier fraction:0.05
+ Averaging method:Mean
+ Variance method:Standard deviation
+ # of deviations:2.0
+ Thresholding method:Otsu
diff -r 000000000000 -r 2005f8058036 test-data/image_math_1.cppipe
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/image_math_1.cppipe Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,112 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:7
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input image:DNA
+ Name the primary objects to be identified:Nucleus
+ Typical diameter of objects, in pixel units (Min,Max):15,200
+ Discard objects outside the diameter range?:Yes
+ Discard objects touching the border of the image?:Yes
+ Method to distinguish clumped objects:Intensity
+ Method to draw dividing lines between clumped objects:Intensity
+ Size of smoothing filter:10
+ Suppress local maxima that are closer than this minimum allowed distance:7.0
+ Speed up by using lower-resolution image to find local maxima?:Yes
+ Fill holes in identified objects?:After both thresholding and declumping
+ Automatically calculate size of smoothing filter for declumping?:Yes
+ Automatically calculate minimum allowed distance between local maxima?:Yes
+ Handling of objects if excessive number of objects identified:Continue
+ Maximum number of objects:500
+ Use advanced settings?:No
+ Threshold setting version:10
+ Threshold strategy:Global
+ Thresholding method:Minimum cross entropy
+ Threshold smoothing scale:1.3488
+ Threshold correction factor:1.0
+ Lower and upper bounds on threshold:0.0,1.0
+ Manual threshold:0.0
+ Select the measurement to threshold with:None
+ Two-class or three-class thresholding?:Two classes
+ Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+ Size of adaptive window:50
+ Lower outlier fraction:0.05
+ Upper outlier fraction:0.05
+ Averaging method:Mean
+ Variance method:Standard deviation
+ # of deviations:2.0
+ Thresholding method:Otsu
+
+ConvertObjectsToImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input objects:Nucleus
+ Name the output image:CellImage
+ Select the color format:Binary (black & white)
+ Select the colormap:Default
+
+ImageMath:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Operation:Add
+ Raise the power of the result by:1.0
+ Multiply the result by:1.0
+ Add to result:0.0
+ Set values less than 0 equal to 0?:Yes
+ Set values greater than 1 equal to 1?:Yes
+ Ignore the image masks?:No
+ Name the output image:ImageAfterMath
+ Image or measurement?:Image
+ Select the first image:DNA
+ Multiply the first image by:1.0
+ Measurement:
+ Image or measurement?:Image
+ Select the second image:CellImage
+ Multiply the second image by:2.0
+ Measurement:
diff -r 000000000000 -r 2005f8058036 test-data/image_math_2.cppipe
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/image_math_2.cppipe Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,112 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:7
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input image:DNA
+ Name the primary objects to be identified:Nucleus
+ Typical diameter of objects, in pixel units (Min,Max):15,200
+ Discard objects outside the diameter range?:Yes
+ Discard objects touching the border of the image?:Yes
+ Method to distinguish clumped objects:Intensity
+ Method to draw dividing lines between clumped objects:Intensity
+ Size of smoothing filter:10
+ Suppress local maxima that are closer than this minimum allowed distance:7.0
+ Speed up by using lower-resolution image to find local maxima?:Yes
+ Fill holes in identified objects?:After both thresholding and declumping
+ Automatically calculate size of smoothing filter for declumping?:Yes
+ Automatically calculate minimum allowed distance between local maxima?:Yes
+ Handling of objects if excessive number of objects identified:Continue
+ Maximum number of objects:500
+ Use advanced settings?:No
+ Threshold setting version:10
+ Threshold strategy:Global
+ Thresholding method:Minimum cross entropy
+ Threshold smoothing scale:1.3488
+ Threshold correction factor:1.0
+ Lower and upper bounds on threshold:0.0,1.0
+ Manual threshold:0.0
+ Select the measurement to threshold with:None
+ Two-class or three-class thresholding?:Two classes
+ Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+ Size of adaptive window:50
+ Lower outlier fraction:0.05
+ Upper outlier fraction:0.05
+ Averaging method:Mean
+ Variance method:Standard deviation
+ # of deviations:2.0
+ Thresholding method:Otsu
+
+ConvertObjectsToImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input objects:Nucleus
+ Name the output image:CellImage
+ Select the color format:Binary (black & white)
+ Select the colormap:Default
+
+ImageMath:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Operation:Subtract
+ Raise the power of the result by:1.0
+ Multiply the result by:1.0
+ Add to result:0.0
+ Set values less than 0 equal to 0?:Yes
+ Set values greater than 1 equal to 1?:No
+ Ignore the image masks?:No
+ Name the output image:ImageAfterMath
+ Image or measurement?:Image
+ Select the first image:DNA
+ Multiply the first image by:1.0
+ Measurement:
+ Image or measurement?:Measurement
+ Select the second image:
+ Multiply the second image by:5.0
+ Measurement:FileName_DNA
diff -r 000000000000 -r 2005f8058036 test-data/image_math_3.cppipe
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/image_math_3.cppipe Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,112 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:7
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input image:DNA
+ Name the primary objects to be identified:Nucleus
+ Typical diameter of objects, in pixel units (Min,Max):15,200
+ Discard objects outside the diameter range?:Yes
+ Discard objects touching the border of the image?:Yes
+ Method to distinguish clumped objects:Intensity
+ Method to draw dividing lines between clumped objects:Intensity
+ Size of smoothing filter:10
+ Suppress local maxima that are closer than this minimum allowed distance:7.0
+ Speed up by using lower-resolution image to find local maxima?:Yes
+ Fill holes in identified objects?:After both thresholding and declumping
+ Automatically calculate size of smoothing filter for declumping?:Yes
+ Automatically calculate minimum allowed distance between local maxima?:Yes
+ Handling of objects if excessive number of objects identified:Continue
+ Maximum number of objects:500
+ Use advanced settings?:No
+ Threshold setting version:10
+ Threshold strategy:Global
+ Thresholding method:Minimum cross entropy
+ Threshold smoothing scale:1.3488
+ Threshold correction factor:1.0
+ Lower and upper bounds on threshold:0.0,1.0
+ Manual threshold:0.0
+ Select the measurement to threshold with:None
+ Two-class or three-class thresholding?:Two classes
+ Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+ Size of adaptive window:50
+ Lower outlier fraction:0.05
+ Upper outlier fraction:0.05
+ Averaging method:Mean
+ Variance method:Standard deviation
+ # of deviations:2.0
+ Thresholding method:Otsu
+
+ConvertObjectsToImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input objects:Nucleus
+ Name the output image:CellImage
+ Select the color format:Binary (black & white)
+ Select the colormap:Default
+
+ImageMath:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Operation:Not
+ Raise the power of the result by:
+ Multiply the result by:
+ Add to result:
+ Set values less than 0 equal to 0?:
+ Set values greater than 1 equal to 1?:
+ Ignore the image masks?:No
+ Name the output image:ImageAfterMath
+ Image or measurement?:Image
+ Select the first image:DNA
+ Multiply the first image by:
+ Measurement:
+ Image or measurement?:
+ Select the second image:
+ Multiply the second image by:
+ Measurement:
diff -r 000000000000 -r 2005f8058036 test-data/images/AS_09125_050116030001_D03f00d0.tif
Binary file test-data/images/AS_09125_050116030001_D03f00d0.tif has changed
diff -r 000000000000 -r 2005f8058036 test-data/images/AS_09125_050116030001_D03f00d1.tif
Binary file test-data/images/AS_09125_050116030001_D03f00d1.tif has changed
diff -r 000000000000 -r 2005f8058036 test-data/images/AS_09125_050116030001_D03f00d2.tif
Binary file test-data/images/AS_09125_050116030001_D03f00d2.tif has changed
diff -r 000000000000 -r 2005f8058036 test-data/mask_image.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mask_image.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,61 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+MaskImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B'Keep only nucleoli inside the nuclei\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the input image:DNAdarkholes
+ Name the output image:MaskDNAdarkholes
+ Use objects or an image as a mask?:Objects
+ Select object for mask:Nuclei
+ Select image for mask:None
+ Invert the mask?:No
diff -r 000000000000 -r 2005f8058036 test-data/measure_granularity.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_granularity.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+MeasureGranularity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Radius\', '- Range\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Image count:1
+ Object count:0
+ Select an image to measure:DNA
+ Subsampling factor for granularity measurements:0.25
+ Subsampling factor for background reduction:0.25
+ Radius of structuring element:10
+ Range of the granular spectrum:16
diff -r 000000000000 -r 2005f8058036 test-data/measure_image_area_occupied.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_area_occupied.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+MeasureImageAreaOccupied:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Hidden:2
+ Measure the area occupied in a binary image, or in objects?:Objects
+ Select objects to measure:Nuclei
+ Select a binary image to measure:None
+ Measure the area occupied in a binary image, or in objects?:Objects
+ Select objects to measure:Nucleoli
+ Select a binary image to measure:None
diff -r 000000000000 -r 2005f8058036 test-data/measure_image_intensity.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_intensity.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,61 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+MeasureImageIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the image to measure:DNA
+ Measure the intensity only from areas enclosed by objects?:No
+ Select the input objects:None
+ Select the image to measure:DNA
+ Measure the intensity only from areas enclosed by objects?:Yes
+ Select the input objects:Nuclei
diff -r 000000000000 -r 2005f8058036 test-data/measure_image_quality.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_quality.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,72 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+MeasureImageQuality:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Calculate metrics for which images?:All loaded images
+ Image count:1
+ Scale count:1
+ Threshold count:1
+ Select the images to measure:
+ Include the image rescaling value?:Yes
+ Calculate blur metrics?:Yes
+ Spatial scale for blur measurements:20
+ Calculate saturation metrics?:Yes
+ Calculate intensity metrics?:Yes
+ Calculate thresholds?:Yes
+ Use all thresholding methods?:No
+ Select a thresholding method:Otsu
+ Typical fraction of the image covered by objects:0.1
+ Two-class or three-class thresholding?:Two classes
+ Minimize the weighted variance or the entropy:Weighted variance
+ Assign pixels in the middle intensity class to the foreground or the background?:Foreground
diff -r 000000000000 -r 2005f8058036 test-data/measure_object_intensity.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_object_intensity.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,58 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+MeasureObjectIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Hidden:1
+ Select an image to measure:DNA
+ Select objects to measure:Nuclei
diff -r 000000000000 -r 2005f8058036 test-data/measure_object_size.txt
diff -r 000000000000 -r 2005f8058036 test-data/measure_object_size_shape.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_object_size_shape.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,58 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+MeasureObjectSizeShape:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select objects to measure:Nuclei
+ Select objects to measure:Nucleoli
+ Calculate the Zernike features?:Yes
diff -r 000000000000 -r 2005f8058036 test-data/measure_texture.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_texture.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+MeasureTexture:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Texture scale']|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Hidden:1
+ Hidden:1
+ Hidden:1
+ Select an image to measure:DNA
+ Select objects to measure:Nuclei
+ Texture scale to measure:3
+ Measure images or objects?:Objects
diff -r 000000000000 -r 2005f8058036 test-data/relate_objects.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relate_objects.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+RelateObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Parent objects:Nuclei
+ Child objects:Nucleoli
+ Calculate child-parent distances?:Both
+ Calculate per-parent means for all child measurements?:Yes
+ Calculate distances to other parents?:No
+ Do you want to save the children with parents as a new object set?:Yes
+ Name the output object:RelateObjects
diff -r 000000000000 -r 2005f8058036 test-data/save_images.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/save_images.txt Thu Apr 16 05:33:39 2020 -0400
@@ -0,0 +1,71 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ :
+ Filter images?:Images only
+ Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+ Extract metadata?:Yes
+ Metadata data type:Text
+ Metadata types:{}
+ Extraction method count:1
+ Metadata extraction method:Extract from file/folder names
+ Metadata source:File name
+ Regular expression to extract from file name:(?P.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)
+ Regular expression to extract from folder name:(?P.*)
+ Extract metadata from:All images
+ Select the filtering criteria:and (file does contain "")
+ Metadata file location:
+ Match file and image metadata:[]
+ Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Assign a name to:Images matching rules
+ Select the image type:Grayscale image
+ Name to assign these images:DNA
+ Match metadata:[]
+ Image set matching method:Order
+ Set intensity range from:Image metadata
+ Assignments count:1
+ Single images count:0
+ Maximum intensity:255.0
+ Process as 3D?:No
+ Relative pixel spacing in X:1.0
+ Relative pixel spacing in Y:1.0
+ Relative pixel spacing in Z:1.0
+ Select the rule criteria:and (file does startwith "im")
+ Name to assign these images:DNA
+ Name to assign these objects:Cell
+ Select the image type:Grayscale image
+ Set intensity range from:Image metadata
+ Select the image type:Grayscale image
+ Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Do you want to group your images?:Yes
+ grouping metadata count:1
+ Metadata category:Screen
+
+SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+ Select the type of image to save:Image
+ Select the image to save:ImageDisplay
+ Select method for constructing file names:From image filename
+ Select image name for file prefix:DNA
+ Enter single file name:OrigBlue
+ Number of digits:4
+ Append a suffix to the image file name?:Yes
+ Text to append to the image name:_nucleiNumbers
+ Saved file format:tiff
+ Output file location:Default Output Folder\x7Coutput
+ Image bit depth:8-bit integer
+ Overwrite existing files without warning?:Yes
+ When to save:Every cycle
+ Record the file and path information to the saved image?:No
+ Create subfolders in the output folder?:No
+ Base image folder:Elsewhere...