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Commit 178666c9 authored by Kai Schleicher's avatar Kai Schleicher
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each script writes its result into its own specific folder

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1_identify_fibers.py
+ 5
− 4
View file @ 178666c9
......@@ -502,12 +502,11 @@ raw_image_calibration = raw.getCalibration()
raw_image_title = fix_BF_czi_imagetitle(raw)
# take care of paths and directories
output_dir = fix_ij_dirs(output_dir)
output_dir = fix_ij_dirs(output_dir) + str(raw_image_title) + "/1_identify_fibers/"
if not os.path.exists( str(output_dir + raw_image_title) ):
os.makedirs( str(output_dir + raw_image_title) )
if not os.path.exists( output_dir ):
os.makedirs( output_dir )
output_dir = str( output_dir + raw_image_title ) + "/"
classifiers_dir = fix_ij_dirs(classifiers_dir)
primary_model = classifiers_dir + "primary.model"
secondary_model = classifiers_dir + "secondary_central_nuclei.model"
......@@ -525,6 +524,8 @@ IJ.log( "solidity = " + str(minSol) + "-" + str(maxSol) )
IJ.log( "feret_ar = " + str(minFAR) + "-" + str(maxFAR) )
IJ.log( "min_feret = " + str(minMinFer) + "-" + str(maxMinFer) )
IJ.log( "ROI expansion [microns] = " + str(enlarge) )
IJ.log( "Membrane channel = " + str(membrane_channel) )
IJ.log( "MHC positive fiber channel = " + str(fiber_channel) )
IJ.log( "sub-tiling = " + str(tiling_factor) )
IJ.log( " -- settings used -- ")
......
2a_central_nuclei_counter.py
+ 7
− 5
View file @ 178666c9
......@@ -19,6 +19,7 @@ import os
#@ String (visibility=MESSAGE, value="<html><b> Welcome to Myosoft - centralized nuclei counter! </b></html>") msg1
#@ File (label="Select fiber-ROIs zip-file", style="file") roi_zip
#@ File (label="Select image file", description="select your image") path_to_image
#@ File (label="Select directory for output", style="directory") output_dir
#@ Boolean (label="close image after processing", description="tick this box when using batch mode", value=False) close_raw
#@ String (visibility=MESSAGE, value="<html><b> shrink ROIs to find nuclei </b></html>") msg3
#@ Float (label="ROI Shrinking factor", value=0.7) shrink
......@@ -62,7 +63,7 @@ def fix_ij_dirs(path):
"""
fixed_path = str(path).replace("\\", "/")
fixed_path = fixed_path + "/"
# fixed_path = fixed_path + "/"
return fixed_path
......@@ -372,10 +373,11 @@ raw_image_calibration = raw.getCalibration()
raw_image_title = fix_BF_czi_imagetitle(raw)
# take care of paths and directories
output_dir = os.path.dirname(str(roi_zip))
input_roi_zip = os.path.basename(str(roi_zip))
output_dir = fix_ij_dirs(output_dir)
input_rois_path = output_dir + input_roi_zip
input_rois_path = fix_ij_dirs( roi_zip )
output_dir = fix_ij_dirs(output_dir) + "/2a_central_nuclei_counter/"
if not os.path.exists( output_dir ):
os.makedirs( output_dir )
# open ROIS and show on image
open_rois_from_zip( rm, input_rois_path )
......
2b_fibertyping.py
+ 13
− 6
View file @ 178666c9
......@@ -19,6 +19,7 @@ import os
#@ String (visibility=MESSAGE, value="<html><b> Welcome to Myosoft! </b></html>") msg1
#@ File (label="Select fiber-ROIs zip-file", style="file") roi_zip
#@ File (label="Select image file", description="select your image") path_to_image
#@ File (label="Select directory for output", style="directory") output_dir
#@ Boolean (label="close image after processing", description="tick this box when using batch mode", value=False) close_raw
#@ String (visibility=MESSAGE, value="<html><b> channel positions in the hyperstack </b></html>") msg5
#@ Integer (label="Fiber staining 1 channel number (0=n.a.)", style="slider", min=0, max=5, value=1) fiber_channel_1
......@@ -64,7 +65,7 @@ def fix_ij_dirs(path):
"""
fixed_path = str(path).replace("\\", "/")
fixed_path = fixed_path + "/"
# fixed_path = fixed_path + "/"
return fixed_path
......@@ -373,11 +374,17 @@ raw_image_calibration = raw.getCalibration()
raw_image_title = fix_BF_czi_imagetitle(raw)
# take care of paths and directories
output_dir = os.path.dirname(str(roi_zip))
output_dir = fix_ij_dirs(output_dir)
# output_dir = os.path.dirname(str(roi_zip))
# output_dir = fix_ij_dirs(output_dir)
input_rois_path = fix_ij_dirs( roi_zip )
output_dir = fix_ij_dirs(output_dir) + "/2b_fibertyping/"
if not os.path.exists( output_dir ):
os.makedirs( output_dir )
# open ROIS and show on image
open_rois_from_zip( rm, str(roi_zip) )
open_rois_from_zip( rm, str(input_rois_path) )
change_all_roi_color(rm, "blue")
show_all_rois_on_image( rm, raw )
......@@ -386,7 +393,7 @@ IJ.log( "Now working on " + str(raw_image_title) )
if raw_image_calibration.scaled() == False:
IJ.log("Your image is not spatially calibrated! Size measurements are only possible in [px].")
IJ.log( " -- settings used -- ")
IJ.log( "Selected fiber-ROIs zip-file = " + str(roi_zip) )
IJ.log( "Selected fiber-ROIs zip-file = " + str(input_rois_path) )
IJ.log( "Fiber staining 1 channel number = " + str(fiber_channel_1) )
IJ.log( "Fiber staining 2 channel number = " + str(fiber_channel_2) )
IJ.log( "Fiber staining 3 channel number = " + str(fiber_channel_3) )
......@@ -397,7 +404,7 @@ IJ.run("Set Measurements...", "area perimeter shape feret's redirect=None decima
IJ.run("Clear Results", "")
measure_in_all_rois( raw, fiber_channel_1, rm )
# loop trhough the fiber channels, check if positive, add info to results table
# loop through the fiber channels, check if positive, add info to results table
all_fiber_channels = [fiber_channel_1, fiber_channel_2, fiber_channel_3]
all_min_fiber_intensities = [min_fiber_intensity_1, min_fiber_intensity_2, min_fiber_intensity_3]
roi_colors = ["green", "orange", "red"]
......
3_manual_rerun.py
+ 5
− 2
View file @ 178666c9
......@@ -24,7 +24,7 @@ def fix_ij_dirs(path):
"""
fixed_path = str(path).replace("\\", "/")
fixed_path = fixed_path + "/"
# fixed_path = fixed_path + "/"
return fixed_path
......@@ -164,7 +164,10 @@ def show_all_rois_on_image(rm, imp):
rm.runCommand(imp,"Show All")
output_dir = fix_ij_dirs(output_dir)
output_dir = fix_ij_dirs(output_dir) + "/3_manual_rerun/"
if not os.path.exists( output_dir ):
os.makedirs( output_dir )
rt.reset()
raw_image_title = fix_BF_czi_imagetitle(raw)
renumber_rois(rm)
......
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