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Changeset 3:69e951528a0b (2024-09-25)

Previous changeset 2:eabdcf6ad900 (2023-11-05)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

removed:
test-data/analyze_particles_masks.gif
test-data/blobs_threshold_ijiso.gif
test-data/dot_blot.jpg
test-data/dot_blot.png
test-data/dot_blot.tiff

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_adjust_threshold_binary_jython_script.py
--- a/imagej2_adjust_threshold_binary_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_adjust_threshold_binary_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -1,18 +1,15 @@
import sys

-from ij import IJ
+from ij import IJ, Prefs

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-10]
-input_file = sys.argv[-9]
-threshold_min = float(sys.argv[-8])
-threshold_max = float(sys.argv[-7])
-method = sys.argv[-6]
-display = sys.argv[-5]
-black_background = sys.argv[-4] == "yes"
-# TODO: this is not being used.
-stack_histogram = sys.argv[-3] == "yes"
+input_file = sys.argv[-8]
+threshold_min = float(sys.argv[-7])
+threshold_max = float(sys.argv[-6])
+method = sys.argv[-5]
+display = sys.argv[-4]
+black_background = sys.argv[-3] == "yes"
output_filename = sys.argv[-2]
output_datatype = sys.argv[-1]

@@ -21,22 +18,34 @@

# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
-image_processor_copy = input_image_plus_copy.getProcessor()
+
+bit_depth = input_image_plus_copy.getBitDepth()
+
+if black_background:
+    Prefs.blackBackground = True
+else:
+    Prefs.blackBackground = False

-# Convert image to binary if necessary.
-if not image_processor_copy.isBinary():
-    # Convert the image to binary grayscale.
-    IJ.run(
-        input_image_plus_copy,
-        "Make Binary",
-        "iterations=1 count=1 edm=Overwrite do=Nothing",
-    )
-# Set the options.
-if black_background:
-    method_str = "%s dark" % method
-else:
-    method_str = method
-IJ.setAutoThreshold(input_image_plus_copy, method_str)
+if method != "Manual":
+    # Set the options.
+    if black_background:
+        method_str = "%s dark" % method
+        suffix = "black"
+    else:
+        method_str = method
+        suffix = ""
+    threshold_min = 1
+    # Set threshold_max based on image bit-depth
+    # For 8-bit images, use 255; for 16-bit images, use 65535
+    if bit_depth == 8:
+        threshold_max = 255  # Default for 8-bit images
+    elif bit_depth == 16:
+        threshold_max = 65535  # Default for 16-bit images
+    else:
+        threshold_max = float('inf')  # General fallback if bit depth is unknown
+
+    IJ.setAutoThreshold(input_image_plus_copy, method_str)
+    IJ.run(input_image_plus_copy, "Convert to Mask", "calculate %s" % suffix)
if display == "red":
     display_mode = "Red"
elif display == "bw":
@@ -44,7 +53,5 @@
elif display == "over_under":
     display_mode = "Over/Under"
IJ.setThreshold(input_image_plus_copy, threshold_min, threshold_max, display_mode)
-# Run the command.
-IJ.run(input_image_plus_copy, "threshold", "")
# Save the ImagePlus object as a new image.
IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_analyze_particles_binary_jython_script.py
--- a/imagej2_analyze_particles_binary_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_analyze_particles_binary_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -1,27 +1,32 @@
import sys

-from ij import IJ
+from ij import IJ, Prefs
from ij.plugin.filter import Analyzer

OPTIONS = ["edm=Overwrite", "iterations=1", "count=1"]

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-14]
-input_file = sys.argv[-13]
-black_background = sys.argv[-12] == "yes"
-size = sys.argv[-11]
-circularity_min = float(sys.argv[-10])
-circularity_max = float(sys.argv[-9])
-show = sys.argv[-8]
-display_results = sys.argv[-7] == "yes"
-all_results = sys.argv[-6] == "yes"
+roi_coordinate_file = sys.argv[-13]
+input_file = sys.argv[-12]
+black_background = sys.argv[-11] == "yes"
+size = sys.argv[-10]
+circularity_min = float(sys.argv[-9])
+circularity_max = float(sys.argv[-8])
+show = sys.argv[-7]
+display_results = sys.argv[-6] == "yes"
exclude_edges = sys.argv[-5] == "yes"
include_holes = sys.argv[-4] == "yes"
output_filename = sys.argv[-3]
output_datatype = sys.argv[-2]
results_path = sys.argv[-1]

+
+if black_background:
+    Prefs.blackBackground = True
+else:
+    Prefs.blackBackground = False
+
# Open the input image file.
input_image_plus = IJ.openImage(input_file)

@@ -42,9 +47,32 @@
     IJ.run(input_image_plus_copy, "Make Binary", "")

# Set the options.
-options = ["size=%s" % size]
+options = ["size=%s" % size, "stack"]
circularity_str = "%.3f-%.3f" % (circularity_min, circularity_max)
options.append("circularity=%s" % circularity_str)
+if exclude_edges:
+    options.append("exclude")
+if include_holes:
+    options.append("include")
+
+# If you need the coordinates of ROIs we compute it twice
+if len(roi_coordinate_file) > 0:
+    options2 = list(options)
+    options2.append("show=Overlay")
+    IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options2))
+    ov = input_image_plus_copy.getOverlay()
+    with open(roi_coordinate_file, 'w') as fo:
+        fo.write("shape\tpoints\tlabel\tt\tz\n")
+        for i, roi in enumerate(ov):
+            if roi.getName() is None:
+                roi.name = "ROI_%d" % i
+            poly = roi.getPolygon()
+            x_values = poly.xpoints
+            y_values = poly.ypoints
+            points_coo = ",".join(["(%d,%d)" % (x, y) for x, y in zip(x_values, y_values)])
+            fo.write("Polygon\t%s\t%s\t%d\t%d\n" % (points_coo, roi.getName(), roi.getTPosition(), roi.getZPosition()))
+    analyzer.resetCounter()
+
if show.find("_") >= 0:
     show_str = "[%s]" % show.replace("_", " ")
else:
@@ -52,12 +80,6 @@
options.append("show=%s" % show_str)
if display_results:
     options.append("display")
-    if not all_results:
-        options.append("summarize")
-if exclude_edges:
-    options.append("exclude")
-if include_holes:
-    options.append("include")
# Always run "in_situ".
options.append("in_situ")

@@ -68,6 +90,6 @@
if len(output_filename) > 0:
     # Save the ImagePlus object as a new image.
     IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
-if display_results and len(results_path) > 0:
+if len(results_path) > 0:
     results_table = analyzer.getResultsTable()
     results_table.saveAs(results_path)

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_analyze_skeleton_jython_script.py
--- a/imagej2_analyze_skeleton_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_analyze_skeleton_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -121,7 +121,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-8]
input = sys.argv[-7]
black_background = sys.argv[-6] == "yes"
prune_cycle_method = sys.argv[-5]

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_binary_to_edm_jython_script.py
--- a/imagej2_binary_to_edm_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_binary_to_edm_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -4,7 +4,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-8]
input_file = sys.argv[-7]
iterations = int(sys.argv[-6])
count = int(sys.argv[-5])

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_bunwarpj_raw_transform.xml
--- a/imagej2_bunwarpj_raw_transform.xml Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_bunwarpj_raw_transform.xml Wed Sep 25 16:04:07 2024 +0000

[

@@ -1,4 +1,4 @@
-<tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="@WRAPPER_VERSION@.2">
+<tool id="imagej2_bunwarpj_raw_transform" name="Apply raw transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
@@ -18,10 +18,10 @@

## ImageJ2 requires file extensions to be valid image data types.
#set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
-#set source_with_ext = '.'.join([source_sans_ext, $source_image.ext])
+#set source_with_ext = './' + '.'.join([source_sans_ext, $source_image.ext])
ln -s '$source_image.file_name' '$source_with_ext' &&
#set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
-#set target_with_ext = '.'.join([target_sans_ext, $target_image.ext])
+#set target_with_ext = './' + '.'.join([target_sans_ext, $target_image.ext])
ln -s '$target_image.file_name' '$target_with_ext' &&

bunwarpj -raw_transform
@@ -29,10 +29,6 @@
'$source_with_ext'
'$raw_transformation'
'$source_out'
-&>'$error_log';
-if [[ $? -ne 0 ]]; then
-    cat '$error_log' >&2;
-fi
]]></command>
     <inputs>
         <expand macro="param_target_image"/>
@@ -57,7 +53,7 @@
             <expand macro="test_target_source_images"/>
             <param name="raw_transformation" value="source_raw_transformation.txt"/>
             <param name="source_out_datatype" value="png"/>
-            <output name="source_out" file="raw_trans_registered_source1.png" compare="sim_size"/>
+            <output name="source_out" file="raw_trans_registered_source1.png" compare="image_diff"/>
         </test>
     </tests>
     <help>

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_crop_jython_script.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_crop_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -0,0 +1,55 @@
+import sys
+
+from ij import IJ
+from ij.plugin import Duplicator
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+input_file = sys.argv[-13]
+xleft = int(sys.argv[-12])
+width = int(sys.argv[-11])
+ytop = int(sys.argv[-10])
+height = int(sys.argv[-9])
+first_channel = int(sys.argv[-8])
+last_channel = int(sys.argv[-7])
+first_slice = int(sys.argv[-6])
+last_slice = int(sys.argv[-5])
+first_frame = int(sys.argv[-4])
+last_frame = int(sys.argv[-3])
+output_filename = sys.argv[-2]
+output_datatype = sys.argv[-1]
+
+# Open the input image file.
+input_image_plus = IJ.openImage(input_file)
+
+# Get image dimensions (width, height, nChannels, nSlices, nFrames)
+image_dims = input_image_plus.getDimensions()
+
+# Create a copy of the image.
+input_image_plus_copy = input_image_plus.duplicate()
+
+# Determine if crop in XY is needed:
+if xleft != 0 or width != 0 or ytop != 0 or height != 0:
+    # Need to define a ROI
+    if width == 0:
+        width = image_dims[0] - xleft
+    if height == 0:
+        height = image_dims[1] - ytop
+    input_image_plus_copy.setRoi(xleft, ytop, width, height)
+
+# Replace 0's with default:
+if last_channel == 0:
+    last_channel = image_dims[2]
+if last_slice == 0:
+    last_slice = image_dims[3]
+if last_frame == 0:
+    last_frame = image_dims[4]
+print("Original dimensions:")
+print(image_dims)
+# This will also crop in XY is a ROI has been set
+input_image_plus_copy = Duplicator().run(input_image_plus_copy, first_channel, last_channel, first_slice, last_slice, first_frame, last_frame)
+print("Final dimensions:")
+print(input_image_plus_copy.getDimensions())
+
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_enhance_contrast_jython_script.py
--- a/imagej2_enhance_contrast_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_enhance_contrast_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -4,7 +4,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-7]
input = sys.argv[-6]
equalize_histogram = sys.argv[-5] == "yes"
saturated_pixels = sys.argv[-4]

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_filter_jython_script.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_filter_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -0,0 +1,39 @@
+import sys
+
+from ij import IJ
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+input_file = sys.argv[-8]
+image_datatype = sys.argv[-7]
+filter = sys.argv[-6]
+radius = sys.argv[-5]
+mask = sys.argv[-4]
+light_background = sys.argv[-3]
+dont_substract = sys.argv[-2]
+tmp_output_path = sys.argv[-1]
+
+# Open the input image file.
+image_plus = IJ.openImage(input_file)
+# Create an ImagePlus object for the image.
+image_plus_copy = image_plus.duplicate()
+
+# Perform the analysis on the ImagePlus object.
+try:
+    if filter == "gaussian_blur":
+        IJ.run(image_plus_copy, "Gaussian Blur...", "sigma=%s stack" % radius)
+    elif filter in ["median", "mean", "minimum", "maximum", "variance"]:
+        IJ.run(image_plus_copy, "%s..." % filter.title(), "radius=%s stack" % radius)
+    elif filter == "unsharp_mask":
+        IJ.run(image_plus_copy, "Unsharp Mask...", "radius=%s mask=%s stack" % (radius, mask))
+    elif filter == "top_hat":
+        print("radius=%s %s %s" % (radius, light_background, dont_substract.replace('dont', "don't")))
+        IJ.run(image_plus_copy, "Top Hat...", "radius=%s %s %s stack" % (radius, light_background, dont_substract.replace('dont', "don't")))
+except Exception as e:
+    # This is due to some operations like gaussian_blur which block the script
+    print(e)
+    exit(1)
+# Save the ImagePlus object as a new image.
+IJ.saveAs(image_plus_copy, image_datatype, tmp_output_path)
+# This is due to some operations like gaussian_blur which block the script
+exit(0)

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_find_edges_jython_script.py
--- a/imagej2_find_edges_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_find_edges_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -4,7 +4,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-4]
input = sys.argv[-3]
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_find_maxima_jython_script.py
--- a/imagej2_find_maxima_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_find_maxima_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -6,7 +6,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-10]
input_file = sys.argv[-9]
scale_when_converting = sys.argv[-8] == "yes"
weighted_rgb_conversions = sys.argv[-7] == "yes"
@@ -35,7 +34,7 @@
     if weighted_rgb_conversions:
         options.append("weighted")
# Perform conversion - must happen even if no options are set.
-IJ.run(input_image_plus_copy, "Conversions...", "%s" % " ".join(options))
+IJ.run(input_image_plus_copy, "Conversions...", " %s" % " ".join(options))
if output_type in ["List", "Count"]:
     # W're  generating a tabular file for the output.
     # Set the Find Maxima options.

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_macros.xml
--- a/imagej2_macros.xml Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_macros.xml Wed Sep 25 16:04:07 2024 +0000

@@ -1,19 +1,12 @@
<macros>
-    <token name="@WRAPPER_VERSION@">3.0</token>
+    <token name="@TOOL_VERSION@">20240614</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="fiji_requirements">
         <requirements>
-            <requirement type="package" version="20170530">fiji</requirement>
-            <requirement type="package" version="3.4">grep</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">fiji</requirement>
+            <requirement type="package" version="3.11">grep</requirement>
         </requirements>
     </xml>
-    <xml name="stdio">
-        <stdio>
-            <exit_code range="1:"/>
-            <exit_code range=":-1"/>
-            <regex match="Error:"/>
-            <regex match="Exception:"/>
-        </stdio>
-    </xml>
     <xml name="image_type">
         <param name="image_type" type="select" label="Image type">
             <option value="8-bit_white" selected="true">8-bit white</option>

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_make_binary_jython_script.py
--- a/imagej2_make_binary_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_make_binary_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -4,7 +4,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-8]
input = sys.argv[-7]
iterations = int(sys.argv[-6])
count = int(sys.argv[-5])

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_math_jython_script.py
--- a/imagej2_math_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_math_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -3,8 +3,7 @@
from ij import IJ

# Fiji Jython interpreter implements Python 2.5 which does not
-# provide support for argparse.
-error_log = sys.argv[-8]
+# provide support for argparse.\
input_file = sys.argv[-7]
operation = sys.argv[-6]
expression = sys.argv[-5]
@@ -19,7 +18,6 @@
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]

-print("\nerror_log: %s\n" % str(error_log))
print("\ninput_file: %s\n" % str(input_file))
print("\noperation: %s\n" % str(operation))
print("\nexpression: %s\n" % str(expression))

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_noise_jython_script.py
--- a/imagej2_noise_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_noise_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -1,85 +1,56 @@
import sys

-from ij import IJ
+from ij import IJ, ImagePlus

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-19]
-input_file = sys.argv[-18]
-image_datatype = sys.argv[-17]
-noise = sys.argv[-16]
-standard_deviation = sys.argv[-15]
-radius = sys.argv[-14]
-threshold = sys.argv[-13]
-which_outliers = sys.argv[-12]
-randomj = sys.argv[-11]
-trials = sys.argv[-10]
-probability = sys.argv[-9]
-# Note the spelling - so things don't get confused due to Python lambda function.
-lammbda = sys.argv[-8]
-order = sys.argv[-7]
-mean = sys.argv[-6]
-sigma = sys.argv[-5]
-min = sys.argv[-4]
-max = sys.argv[-3]
-insertion = sys.argv[-2]
+input_file = sys.argv[-8]
+image_datatype = sys.argv[-7]
+noise = sys.argv[-6]
+standard_deviation = sys.argv[-5]
+radius = sys.argv[-4]
+threshold = sys.argv[-3]
+which_outliers = sys.argv[-2]
tmp_output_path = sys.argv[-1]

# Open the input image file.
image_plus = IJ.openImage(input_file)
-bit_depth = image_plus.getBitDepth()
image_type = image_plus.getType()
+is32BITS_GREY = image_type == ImagePlus.GRAY32
# Create an ImagePlus object for the image.
image_plus_copy = image_plus.duplicate()
-# Make a copy of the image.
-image_processor_copy = image_plus_copy.getProcessor()

# Perform the analysis on the ImagePlus object.
-if noise == "add_noise":
-    IJ.run(image_plus_copy, "Add Noise", "")
-elif noise == "add_specified_noise":
-    IJ.run(image_plus_copy, "Add Specified Noise", "standard=&standard_deviation")
-elif noise == "salt_and_pepper":
-    IJ.run(image_plus_copy, "Salt and Pepper", "")
-elif noise == "despeckle":
-    IJ.run(image_plus_copy, "Despeckle", "")
-elif noise == "remove_outliers":
-    IJ.run(
-        image_plus_copy,
-        "Remove Outliers",
-        "radius=&radius threshold=&threshold which=&which_outliers",
-    )
-elif noise == "remove_nans":
-    IJ.run(image_plus_copy, "Remove NaNs", "")
-elif noise == "rof_denoise":
-    IJ.run(image_plus_copy, "ROF Denoise", "")
-elif noise == "randomj":
-    if randomj == "randomj_binomial":
+try:
+    if noise == "add_noise":
+        IJ.run(image_plus_copy, "Add Noise", "")
+    elif noise == "add_specified_noise":
+        IJ.run(image_plus_copy, "Add Specified Noise...", "standard=%s" % standard_deviation)
+    elif noise == "salt_and_pepper":
+        IJ.run(image_plus_copy, "Salt and Pepper", "")
+    elif noise == "despeckle":
+        IJ.run(image_plus_copy, "Despeckle", "")
+    elif noise == "remove_outliers":
         IJ.run(
             image_plus_copy,
-            "RandomJ Binomial",
-            "trials=&trials probability=&probability insertion=&insertion",
-        )
-    elif randomj == "randomj_exponential":
-        IJ.run(
-            image_plus_copy,
-            "RandomJ Exponential",
-            "lambda=&lammbda insertion=&insertion",
+            "Remove Outliers...",
+            "radius=%s threshold=%s which=%s" % (radius, threshold, which_outliers)
         )
-    elif randomj == "randomj_gamma":
-        IJ.run(image_plus_copy, "RandomJ Gamma", "order=&order insertion=&insertion")
-    elif randomj == "randomj_gaussian":
-        IJ.run(
-            image_plus_copy,
-            "RandomJ Gaussian",
-            "mean=&mean sigma=&sigma insertion=&insertion",
-        )
-    elif randomj == "randomj_poisson":
-        IJ.run(image_plus_copy, "RandomJ Poisson", "mean=&mean insertion=&insertion")
-    elif randomj == "randomj_uniform":
-        IJ.run(
-            image_plus_copy, "RandomJ Uniform", "min=&min max=&max insertion=&insertion"
-        )
-
+    elif noise == "remove_nans":
+        if is32BITS_GREY:
+            IJ.run(image_plus_copy, "Remove NaNs...", "")
+        else:
+            raise Exception("Remove NaNs can only be applied to 32bits grey images.")
+    elif noise == "rof_denoise":
+        if is32BITS_GREY:
+            IJ.run(image_plus_copy, "ROF Denoise", "")
+        else:
+            raise Exception("ROF Denoise can only be applied to 32bits grey images.")
+except Exception as e:
+    # This is due to some operations like remove_outliers and despeckle which block the script
+    print(e)
+    exit(1)
# Save the ImagePlus object as a new image.
IJ.saveAs(image_plus_copy, image_datatype, tmp_output_path)
+# This is due to some operations like remove_outliers and despeckle which block the script
+exit(0)

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_shadows_jython_script.py
--- a/imagej2_shadows_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_shadows_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -4,7 +4,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-5]
input_file = sys.argv[-4]
direction = sys.argv[-3]
tmp_output_path = sys.argv[-2]

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_sharpen_jython_script.py
--- a/imagej2_sharpen_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_sharpen_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -4,7 +4,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-4]
input_file = sys.argv[-3]
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_skeletonize3d_jython_script.py
--- a/imagej2_skeletonize3d_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_skeletonize3d_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -4,7 +4,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-5]
input_file = sys.argv[-4]
black_background = sys.argv[-3] == "yes"
tmp_output_path = sys.argv[-2]

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_smooth_jython_script.py
--- a/imagej2_smooth_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_smooth_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

diff -r eabdcf6ad900 -r 69e951528a0b imagej2_watershed_binary_jython_script.py
--- a/imagej2_watershed_binary_jython_script.py Sun Nov 05 10:50:30 2023 +0000
+++ b/imagej2_watershed_binary_jython_script.py Wed Sep 25 16:04:07 2024 +0000

[

@@ -4,7 +4,6 @@

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
-error_log = sys.argv[-5]
input = sys.argv[-4]
black_background = sys.argv[-3] == "yes"
tmp_output_path = sys.argv[-2]
@@ -30,7 +29,7 @@
IJ.run(input_image_plus_copy, "Make Binary", "")

# Run the command.
-IJ.run(input_image_plus_copy, "Watershed", "")
+IJ.run(input_image_plus_copy, "Watershed", "stack")

# Save the ImagePlus object as a new image.
IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)

diff -r eabdcf6ad900 -r 69e951528a0b test-data/add_specified_noise.gif

Binary file test-data/add_specified_noise.gif has changed

diff -r eabdcf6ad900 -r 69e951528a0b test-data/analyze_particles_bareoutlines.gif

Binary file test-data/analyze_particles_bareoutlines.gif has changed

diff -r eabdcf6ad900 -r 69e951528a0b test-data/analyze_particles_masks.gif

Binary file test-data/analyze_particles_masks.gif has changed

diff -r eabdcf6ad900 -r 69e951528a0b test-data/analyze_particles_outlines.gif

Binary file test-data/analyze_particles_outlines.gif has changed

diff -r eabdcf6ad900 -r 69e951528a0b test-data/analyze_particles_overlaymasks.gif

Binary file test-data/analyze_particles_overlaymasks.gif has changed

diff -r eabdcf6ad900 -r 69e951528a0b test-data/analyze_particles_rois.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/analyze_particles_rois.tabular Wed Sep 25 16:04:07 2024 +0000

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/blobs_crop_top50.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/blobs_crop_width50.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/blobs_threshold_8-255.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/blobs_threshold_default.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/blobs_threshold_huang_dark.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/blobs_threshold_ijiso.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/blobs_threshold_percentile.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/composed_raw_elastic_transformation_full.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/composed_raw_elastic_transformation_full.txt Wed Sep 25 16:04:07 2024 +0000

b'@@ -0,0 +1,294 @@\n+Width=144\n+Height=144\n+\n+X Trans -----------------------------------\n+ -8.356784649818302 -7.197224454983437 -6.007291128456463 -4.78857035976083 -3.542648755368276 -2.27111292175059 -0.9755494653795207 0.34245500727314293 1.6813138897356357 3.0394405755361955 4.415248458203067 5.807150931264452 7.21356138824859 6.722616523231703 7.982832965851492 9.241901922762699 10.500157904929564 11.755439850906992 13.007881998138114 14.257818796273467 15.503597042436024 16.7441831444607 17.979203521782882 19.209729191621175 20.434924351265607 21.653927817871562 22.868018271403987 24.077212618583225 25.28220858222662 26.482822213238034 27.68108269563495 28.876976885081163 30.071735843481154 31.267312088467172 32.461884574486334 33.6540253250871 34.84451070010306 36.032159052340404 37.21731193936262 38.40098887470948 39.58514301848773 40.7697991777691 41.95621659878733 43.14336916337468 44.332762755666245 45.52368427263207 46.71616063628192 47.9102587132078 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diff -r eabdcf6ad900 -r 69e951528a0b test-data/composed_raw_transformation_full.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/composed_raw_transformation_full.txt Wed Sep 25 16:04:07 2024 +0000

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/confocal_analyze_particles.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/confocal_analyze_particles.tabular Wed Sep 25 16:04:07 2024 +0000

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/confocal_analyze_particles_rois.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/confocal_analyze_particles_rois.tabular Wed Sep 25 16:04:07 2024 +0000

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/raw_transformation_full.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw_transformation_full.txt Wed Sep 25 16:04:07 2024 +0000

b'@@ -0,0 +1,294 @@\n+Width=144\n+Height=144\n+\n+X Trans -----------------------------------\n+ 4.176715938136983 5.028059425766952 5.848163112344083 6.625286081420434 7.346949869450837 7.999993504600507 8.570638908853306 9.044622789513964 9.413506255387968 9.681218421492703 9.854312101993061 9.940614113498254 9.949133680349874 9.889960336823316 9.774150445497835 9.613603978540679 9.420928827203937 9.209297594621251 8.99229520815497 8.783758029488393 8.597605040212112 8.447661785513965 8.347477892926463 8.310139148227263 8.348075306899938 8.472865046334638 8.695039719264653 9.02388784955587 9.467262612735961 10.031394859423866 10.720714562420634 11.537683888429232 12.482635931423559 13.548553680644847 14.713909933407903 15.955437681044362 17.250615997032845 18.57910317041673 19.924588848162042 21.273131961240793 22.61287165006273 23.933978509626925 25.228599373795102 26.49079330268239 27.7164571781934 28.90324005022652 30.050446065539795 31.15892642005994 32.23096128077027 33.27013301056534 34.28119229030748 35.269918863348025 36.24297862912084 37.20777868670669 38.172321680760554 39.14506043617836 40.134753390327724 41.15032074914446 42.20070061327572 43.29470355140843 44.44086325080732 45.64727996412613 46.921452516062644 48.27009365995084 49.69892261951472 51.21242468486518 52.81308002996115 54.5006890705208 56.27295866194047 58.12547164246331 60.05155284704986 62.042126167374654 64.0853963435782 66.16300087019144 68.25096023630147 70.32434810515224 72.35799991286407 74.32708587789452 76.20772360258024 77.97761366869307 79.61667819048832 81.10767966466686 82.43679584207585 83.59412588149885 84.57410381192264 85.37579734320398 86.0030732794589 86.46461509691974 86.77378348443933 86.94831659732299 87.00987319114694 86.98342840026854 86.89653840770765 86.77849631690853 86.65940540750502 86.56678652831073 86.51894680093264 86.52962234401939 86.6091568313555 86.76444343256262 86.99795950541491 87.30767458029689 87.6887773859162 88.1343150744824 88.63573469192004 89.18339795340363 89.76705660855026 90.37627810648544 91.00098259921862 91.63313750582321 92.26649727091988 92.89592945322954 93.51736271382487 94.12771798912087 94.72482575123138 95.30733544608778 95.87462173881887 96.42669102951422 96.9640907767786 97.48782343666693 97.99926625358638 98.50009769694455 98.99223099750193 99.47775497987517 99.95888219552717 100.43790422009906 100.91715387889398 101.39897409567641 101.8856930154123 102.37960502529904 102.88295728576551 103.39794138037603 103.92668969786209 104.47127616862906 105.03372099039578 105.61599899198129 106.2200512999695 106.84779998979062 107.50116542083198 108.1820859751434 108.89253994223978 109.63456932007529 110.41030533674008 111.22199287092927 \n+ 4.419557770482417 5.27081665328943 6.089884477973564 6.864617423433236 7.58211191931238 8.228765517486593 8.790349543698422 9.252193879414877 9.606403124097358 9.8574446972737 10.012252733626926 10.079097632567096 10.067484069087474 9.988036761486226 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140.86911184204715 140.92038668238638 140.95469057503053 140.96951446175183 \n+ 136.47128086107668 136.7647212366112 137.09257955898585 137.45244030061366 137.84178817314864 138.25801861080936 138.69844448570618 139.16030362004625 139.64076716336413 140.13694888129027 140.64591537702537 141.16469723830411 141.69030107199748 142.21972235649292 142.7499590095462 143.27802553739224 143.8009676005144 144.31587680358044 144.81990549256307 145.31028132185114 145.78432133896519 146.23944532498265 146.6731881254606 147.08321070988862 147.4673097077118 147.82342518575646 148.1497532260637 148.44517260159793 148.70888980473805 148.9402693649705 149.13881819510797 149.30416655832204 149.43604583881495 149.53426341914945 149.59867502302262 149.6291549350847 149.62557137943307 149.58856731644082 149.52026608135293 149.42281660859848 149.29821829294679 149.14833393227818 148.9749036871724 148.77955958387102 148.56384015461515 148.3292048735639 148.07704810673272 147.80871235013433 147.52550058127326 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diff -r eabdcf6ad900 -r 69e951528a0b test-data/regenerate_outputs.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/regenerate_outputs.sh Wed Sep 25 16:04:07 2024 +0000

b"@@ -0,0 +1,204 @@\n+source $(dirname $(dirname $(which conda)))/etc/profile.d/conda.sh\n+conda_env=mulled-v1-9e9e3735532d83dd44ff0f622055395263f964e81ca8113d4dfa7e133e3156bf\n+conda activate $conda_env\n+# Adjust threshold\n+# Test 1\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 255.0 'Default' 'red' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_default.gif' 'gif'\n+# Test 2\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 255.0 'Percentile' 'over_under' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_percentile.gif' 'gif'\n+# Test 3\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 255.0 'Huang' 'bw' 'yes' 'tools/image_processing/imagej2/test-data/blobs_threshold_huang_dark.gif' 'gif'\n+# Test 4\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 8.0 255.0 'Manual' 'bw' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_8-255.gif' 'gif'\n+# Test 5\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 0.0 8.0 'Manual' 'bw' 'no' 'tools/image_processing/imagej2/test-data/blobs_threshold_0-8.gif' 'gif'\n+# Test 6\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_adjust_threshold_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel.tif' 0.0 255.0 'Default' 'bw' 'yes' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'tiff'\n+\n+\n+# Analyze particles\n+# Test 1\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' '' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Nothing' 'yes' 'no' 'no' '' '' 'tools/image_processing/imagej2/test-data/analyze_particles_nothing.tabular'\n+# Test 2\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' '' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Outlines' 'no' 'no' 'no' 'tools/image_processing/imagej2/test-data/analyze_particles_outlines.gif' 'gif' ''\n+# Test 3\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' '' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Bare_Outlines' 'no' 'yes' 'yes' 'tools/image_processing/imagej2/test-data/analyze_particles_bareoutlines.gif' 'gif' ''\n+# Test 4\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/analyze_particles_rois.tabular' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' '0-Infinity' 0.0 1.0 'Overlay_Masks' 'yes' 'no' 'no' 'tools/image_processing/imagej2/test-data/analyze_particles_overlaymasks.gif' 'gif' 'tools/image_processing/imagej2/test-data/analyze_particles_nothing.tabular'\n+# Test 5\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal_analyze_particles_rois.tabular' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'yes' '0-Infinity' 0.0 1.0 'Overlay_Masks' 'yes' 'no' 'no' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default_"..b"imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Min' 'None' 'None' 255.0 'tools/image_processing/imagej2/test-data/blobs_min.gif' 'gif'\n+# Test 3\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Log' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/blobs_log.gif' 'gif'\n+# Test 4\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Square' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/blobs_square.gif' 'gif'\n+# Test 5\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_math_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Macro' 'v=v+50*sin(d/17)' 'None' 'None' 'tools/image_processing/imagej2/test-data/blobs_macro.gif' 'gif'\n+\n+# Noise\n+# Test 1\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'add_specified_noise' 5.0 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/add_specified_noise.gif'\n+# Test 2\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'despeckle' 'None' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/despeckle.gif'\n+# Test 3\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'remove_outliers' 'None' '10.0' '1' 'Bright' 'tools/image_processing/imagej2/test-data/remove_outliers.gif'\n+# Test 4 fails\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_noise_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'gif' 'remove_nans' 'None' 'None' 'None' 'None' 'tools/image_processing/imagej2/test-data/remove_nans.gif'\n+\n+# Shadows\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_shadows_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'Northwest' 'tools/image_processing/imagej2/test-data/blobs_northwest.gif' 'gif'\n+\n+# Sharpen\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_sharpen_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_sharpen.gif' 'gif'\n+\n+# Skeletonized 3D\n+# Test 1\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_skeletonize3d_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 'tools/image_processing/imagej2/test-data/skeletonized_blobs.gif' 'gif'\n+# Test 2\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_skeletonize3d_jython_script.py' 'tools/image_processing/imagej2/test-data/clown.jpg' 'no' 'tools/image_processing/imagej2/test-data/skeletonized_clown.jpg' 'jpg'\n+\n+# Smooth\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_smooth_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'tools/image_processing/imagej2/test-data/blobs_smooth.gif' 'gif'\n+\n+# Watershed\n+# Test 1\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_watershed_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/blobs.gif' 'no' 'tools/image_processing/imagej2/test-data/blobs_watershed_binary.gif' 'gif'\n+# Test 2\n+ImageJ --ij2 --headless --debug --jython 'tools/image_processing/imagej2/imagej2_watershed_binary_jython_script.py' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'yes' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_default_threshold_watershed.tiff' 'tiff'\n"

diff -r eabdcf6ad900 -r 69e951528a0b test-data/registered_source1.png

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/registered_source1_forced1cpu.png

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/registered_source2.png

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/registered_source2_forced1cpu.png

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/registered_target1.png

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/registered_target1_forced1cpu.png

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/registered_target2.png

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/registered_target2_forced1cpu.png

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/remove_outliers.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/shortest_branch_all_yes.tabular
--- a/test-data/shortest_branch_all_yes.tabular Sun Nov 05 10:50:30 2023 +0000
+++ b/test-data/shortest_branch_all_yes.tabular Wed Sep 25 16:04:07 2024 +0000

@@ -2,7 +2,7 @@
1 0 2 0 1 2.414 0 0 2.414 2.414 1 59 0
1 0 2 0 0 1.000 0 0 1.000 1.000 4 91 0
0 0 1 0 0 0.000 0 0 0.000 0.000 5 43 0
-143 75 40 144 918 9.176 61 9 96.113 277.930 161 0 0
+143 75 40 144 918 9.873 61 9 96.113 277.930 161 0 0
0 0 1 0 0 0.000 0 0 0.000 0.000 5 80 0
0 0 1 0 0 0.000 0 0 0.000 0.000 6 53 0
0 0 1 0 0 0.000 0 0 0.000 0.000 6 67 0
@@ -18,7 +18,7 @@
1 0 2 0 3 4.414 0 0 4.414 4.414 38 91 0
0 0 1 0 0 0.000 0 0 0.000 0.000 39 88 0
1 0 2 0 3 5.657 0 0 5.657 5.657 49 111 0
-5 2 4 2 97 23.182 2 0 58.385 100.770 92 174 0
+5 2 4 2 97 23.382 2 0 58.385 100.770 92 174 0
0 0 1 0 0 0.000 0 0 0.000 0.000 65 31 0
0 0 1 0 0 0.000 0 0 0.000 0.000 66 175 0
1 0 2 0 4 5.828 0 0 5.828 5.828 88 42 0
@@ -27,15 +27,15 @@
0 0 1 0 0 0.000 0 0 0.000 0.000 95 44 0
1 0 2 0 0 1.000 0 0 1.000 1.000 105 14 0
0 0 1 0 0 0.000 0 0 0.000 0.000 104 20 0
-262 117 105 266 957 5.803 65 37 34.142 352.779 279 50 0
-96 43 31 104 373 6.437 25 11 34.142 212.675 192 110 0
+262 117 105 266 957 6.493 65 37 34.142 352.779 279 50 0
+96 43 31 104 373 7.278 25 11 36.971 212.675 192 110 0
0 0 1 0 0 0.000 0 0 0.000 0.000 121 35 0
0 0 1 0 0 0.000 0 0 0.000 0.000 132 54 0
1 0 2 0 0 1.000 0 0 1.000 1.000 135 53 0
0 0 1 0 0 0.000 0 0 0.000 0.000 138 116 0
0 0 1 0 0 0.000 0 0 0.000 0.000 138 124 0
-22 11 10 24 151 9.834 10 1 20.728 116.633 207 123 0
-5 2 4 2 44 12.285 2 0 26.799 52.184 176 174 0
+22 11 10 24 151 10.374 10 1 20.728 116.633 207 123 0
+5 2 4 2 44 12.568 2 0 26.799 52.184 176 174 0
0 0 1 0 0 0.000 0 0 0.000 0.000 156 54 0
0 0 1 0 0 0.000 0 0 0.000 0.000 162 61 0
0 0 1 0 0 0.000 0 0 0.000 0.000 163 56 0
@@ -150,7 +150,7 @@
0 0 1 0 0 0.000 0 0 0.000 0.000 287 108 0
1 0 2 0 1 2.414 0 0 2.414 2.414 289 122 0
0 0 1 0 0 0.000 0 0 0.000 0.000 287 134 0
-13 6 8 10 55 5.956 6 0 20.899 68.184 309 78 0
+13 6 8 10 55 6.590 6 0 20.899 68.184 309 78 0
0 0 1 0 0 0.000 0 0 0.000 0.000 288 69 0
0 0 1 0 0 0.000 0 0 0.000 0.000 288 75 0
1 0 2 0 0 1.000 0 0 1.000 1.000 288 92 0

diff -r eabdcf6ad900 -r 69e951528a0b test-data/shortest_branch_basic.tabular
--- a/test-data/shortest_branch_basic.tabular Sun Nov 05 10:50:30 2023 +0000
+++ b/test-data/shortest_branch_basic.tabular Wed Sep 25 16:04:07 2024 +0000

@@ -2,7 +2,7 @@
1 0 2 0 1 2.414 0 0 2.414
1 0 2 0 0 1.000 0 0 1.000
0 0 1 0 0 0.000 0 0 0.000
-143 75 40 144 918 9.176 61 9 96.113
+143 75 40 144 918 9.873 61 9 96.113
0 0 1 0 0 0.000 0 0 0.000
0 0 1 0 0 0.000 0 0 0.000
0 0 1 0 0 0.000 0 0 0.000
@@ -18,7 +18,7 @@
1 0 2 0 3 4.414 0 0 4.414
0 0 1 0 0 0.000 0 0 0.000
1 0 2 0 3 5.657 0 0 5.657
-5 2 4 2 97 23.182 2 0 58.385
+5 2 4 2 97 23.382 2 0 58.385
0 0 1 0 0 0.000 0 0 0.000
0 0 1 0 0 0.000 0 0 0.000
1 0 2 0 4 5.828 0 0 5.828
@@ -27,15 +27,15 @@
0 0 1 0 0 0.000 0 0 0.000
1 0 2 0 0 1.000 0 0 1.000
0 0 1 0 0 0.000 0 0 0.000
-262 117 105 266 957 5.803 65 37 34.142
-96 43 31 104 373 6.437 25 11 34.142
+262 117 105 266 957 6.493 65 37 34.142
+96 43 31 104 373 7.278 25 11 36.971
0 0 1 0 0 0.000 0 0 0.000
0 0 1 0 0 0.000 0 0 0.000
1 0 2 0 0 1.000 0 0 1.000
0 0 1 0 0 0.000 0 0 0.000
0 0 1 0 0 0.000 0 0 0.000
-22 11 10 24 151 9.834 10 1 20.728
-5 2 4 2 44 12.285 2 0 26.799
+22 11 10 24 151 10.374 10 1 20.728
+5 2 4 2 44 12.568 2 0 26.799
0 0 1 0 0 0.000 0 0 0.000
0 0 1 0 0 0.000 0 0 0.000
0 0 1 0 0 0.000 0 0 0.000
@@ -150,7 +150,7 @@
0 0 1 0 0 0.000 0 0 0.000
1 0 2 0 1 2.414 0 0 2.414
0 0 1 0 0 0.000 0 0 0.000
-13 6 8 10 55 5.956 6 0 20.899
+13 6 8 10 55 6.590 6 0 20.899
0 0 1 0 0 0.000 0 0 0.000
0 0 1 0 0 0.000 0 0 0.000
1 0 2 0 0 1.000 0 0 1.000

diff -r eabdcf6ad900 -r 69e951528a0b test-data/source_elastic_transformation_forced1cpu_out_full.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/source_elastic_transformation_forced1cpu_out_full.txt Wed Sep 25 16:04:07 2024 +0000

@@ -0,0 +1,19 @@
+Intervals=4
+
+X Coeffs -----------------------------------
+    -54.0016323325568    -24.55313914003933     9.998378808715369     46.75364792905647     82.81339463633314    119.65671403007485    158.76270120981096
+   -50.83339149878828   -18.681337906130345     37.17883919175264    12.345198999048506     24.77206071041781     97.97412790389771    155.78421869117355
+  -27.929816443724082    49.276999890632126      36.1275114393808     14.75760213419734     9.594845999044615    154.04607396012295    222.05804605430535
+   -9.439167783998862     37.12324241599431     48.73717535550337     63.59070238727008     6.551668091613555     119.5935291038009    158.64847980599265
+   -8.415920987887967    19.182085970213276     89.61484235977517     88.26966501794124    32.788077608672424     132.5037156161929    160.37829930526004
+   -31.71446728510298    11.403380281357434      87.1527845269043      41.0061258664103    18.375036656301404     151.3216275398897    162.14248931362886
+   -36.33357650876076    -2.997067006070702    24.224980747085667     52.94713777251041     90.78409317136875    128.45213257281344     164.4624484013269
+
+Y Coeffs -----------------------------------
+   -35.58508171011618    -35.52735570756093   -35.159196828706726    -29.70750167634807   -28.923802662244935   -34.504255822335935   -35.243494145461135
+   -1.242192601470532     29.46509876064867    -2.312247460503201    10.484826852565131    18.756383154741464    45.881731350540406    -0.621787824102949
+   30.981455595654854    36.951471554766314    3.9820133989773163     7.976064243908333    -7.830691435689818    41.541448554600954    31.732801175989525
+   58.283948016581554   -22.165321992984115    22.635703622205753     8.955455276732383     16.06491478568108    30.317438854555434     60.33829204610447
+    95.46258300786052     43.02756729709696    14.126605325220126     44.78649034596007   -16.764126369901938     35.95147733367494     96.44151384896905
+   130.87735480918948    195.59287946182124    -3.550292865530671   -7.0509958709770295    110.60475571422396    134.61412452223453    130.93519990666056
+    170.4874708714955    161.78056879140948     149.6874025532559    142.17277360792374    150.66515020927875    162.24110899673795    167.44089341269517

diff -r eabdcf6ad900 -r 69e951528a0b test-data/source_elastic_transformation_out_full.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/source_elastic_transformation_out_full.txt Wed Sep 25 16:04:07 2024 +0000

@@ -0,0 +1,19 @@
+Intervals=4
+
+X Coeffs -----------------------------------
+   -37.57669097094904   -3.2271717112514677    30.729561477029474     64.92853072664484    101.26040164233771    134.24138071120504    170.62530571165195
+   -36.40440156764347    -5.950917668399802     43.12656676959308    129.82569373508457     79.23025904056314    101.33109010989303    167.76122399799928
+   -31.99153804062628   -28.228263165717934    108.82281688201007    135.71408978799562    119.88724905944063    115.66219769238425    162.57204585958897
+   -28.76756806285075   -31.072774597932003    149.06671190151698      82.6873796775864     85.83238257129669    102.22408316121394    159.69418492654307
+   -31.16195930727015     39.81052685166829    111.01894213555936    50.843519487267514      71.5843384687527    104.97466705130167    163.76405482898355
+   -34.99727113400996     51.46458209552406    45.814658605380856    127.80078869884827     61.64396676556593     133.5425482462486    169.78763924597007
+  -36.096062903195644   -1.3094687517365522    33.017918855761025      67.2410292328903    101.71479169324449    136.77836848505723     172.7709218565622
+
+Y Coeffs -----------------------------------
+  -20.613508471150247    -17.30904642115659   -13.074039899257977    -12.82208593159747   -21.466781544318113   -31.576707217758816     -35.7204434322585
+   15.694660075623595    29.090244174855332     99.26325690063715     65.87761638249009     60.80790866211655     7.118793613938786   -2.7030258778256626
+     48.4395231974389    20.580542086433006    123.69933199668453     35.70058582463237     48.91160104418716    49.319772349263886     28.24944770390918
+      79.139639872897    28.260304680883564    39.217991856988554     96.98206627187832    122.99790587109494      81.5469103601955     58.57040400869205
+   112.30429273541326    -31.84451342578042    150.53549831852334     93.43230937892993    105.20787588035367     55.33493688123222     89.69326973226897
+   140.48429880851842    54.844800662935505    136.50939139083195    102.42949280502454     96.70614159439262    152.55152439131024      123.051471570386
+   174.17481704462756    171.41787868079226    167.26939245818923     162.8915210072307    159.44642695832863     158.1150765995069     160.0784362187891

diff -r eabdcf6ad900 -r 69e951528a0b test-data/target_elastic_transformation_forced1cpu_out_full.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/target_elastic_transformation_forced1cpu_out_full.txt Wed Sep 25 16:04:07 2024 +0000

@@ -0,0 +1,19 @@
+Intervals=4
+
+X Coeffs -----------------------------------
+   -53.01255704273572   -13.904078412237368     42.28779020312449      49.2241689610889     43.17391161793351     57.12681204296706     93.96096797426937
+  -25.399961768058898     78.11666674988406     47.11538040963914     53.34193146612398     48.19823124809444    51.578486863081025     62.97102702637055
+    74.83364233868025     44.94785732629138     52.59528959805901    54.543817794946555     55.63349375544408     54.50269211372439     47.62502458222461
+   33.696803979050756    58.895615990105675    52.374827040837616     52.52362439850934     51.96459926850969     52.12346709150518     53.22425479912784
+   54.024299911223764     50.97110502497963    53.313115679853226    54.079338788140554    53.975969688179475     55.36463923686487     50.69775408987581
+    61.68987727495051    53.368672489805554     53.49515507648402      51.6321049622464    53.937756626103216     47.83395036978562     64.92582731507672
+    44.35275725127058     53.31850095476804     55.39104510610701     55.66877435102513     55.41166434382368    57.831591051064564    153.61852412379244
+
+Y Coeffs -----------------------------------
+    18.93646011405667    18.932358073393257   -45.807304697888824    12.943663336359961    -6.327036285964463   -27.325046787074903    -28.68009130761568
+    69.72517425473397    18.951944929866418    -54.51191955826718    12.603632065405728     33.43481269330889      140.609614099701    10.728187982256344
+    132.0711970793583    186.36333833664528    184.49603949633777     187.1901604174391    158.07455291450418    198.26170431915625     69.02399552934537
+   152.52702215817044    151.40906569438428    144.41347160527243    148.75680143207387    154.16175661350192    147.09841734177542     144.8860096284916
+   161.22035237120292     158.6171876686065    166.13338308434305     159.7364739623931    160.15750889578624    161.60800126111627    174.81126607209526
+   162.71033090716813    159.95948678510726    149.08911488413267    159.40987351626924    154.10612131309117    156.49431897610225    143.43506000431748
+   143.12909756515404     143.0695229580525     166.0176933508692    144.57111777572015    160.84062396633618    157.42735871635645    133.65686564157454

diff -r eabdcf6ad900 -r 69e951528a0b test-data/target_elastic_transformation_out_full.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/target_elastic_transformation_out_full.txt Wed Sep 25 16:04:07 2024 +0000

@@ -0,0 +1,19 @@
+Intervals=4
+
+X Coeffs -----------------------------------
+   -2.334540491984048    19.197617253297445    14.143262861788983    39.463628125651084     53.54110718736474     77.63432486663321    122.01213769363304
+   18.940100807668394     9.376702061674932     11.32031302209601     9.081414015093257    -19.34191364999764    24.182277174612462    27.994218490639234
+    39.45486659902765      9.40454198383603    22.230846242507905 -0.002478065318311816     73.57478566130307     58.77280036887933     48.90850943566863
+    17.00000657714807    -23.31776136556256    12.541111571022608    7.2459754632090405    59.934726035072856    30.713987461586505     72.32572780611264
+    33.22276292665229   -13.918601953887327   -34.657944692759926    163.25596555413682     65.69636617127611   -2.7667070647362673    105.81487278594533
+    85.11817751007291    120.33953953049102     81.34418995521429      -66.726377368089    18.860324896215854     34.34945385032887     70.51661433028738
+   36.883847445857576     76.35165890505894     6.516561676315538   -20.970133083731874    125.46655281183332    -2.448523111647684    114.79339566399392
+
+Y Coeffs -----------------------------------
+-0.031617394190528676    21.091295827183185     40.99488267737779    133.42310018352737     39.66065981177224    18.453503965110798     18.87752372262639
+    49.43431409316814    119.43278503821342     91.66849730571954     79.91925555046383    106.43225673511903     154.1232341123354     68.50164250154936
+    99.83206171058087     92.97764797169073    103.64352162659048    102.51390748210636      92.4692722023774   -4.7866682215833904     63.31241523442766
+   62.479566052595004      -197.59219058435     99.97143069942541     77.04940775782963   -2.4521487960395176    113.09283045524303     65.44319987491002
+   132.61392700107905     55.19320373443639     259.1024942673179     139.4197212963076     90.08817257816702    111.80227388699566     73.97266542006085
+   126.91904730761814     73.28185948235975     63.29420821019147     75.30231636943734     88.05821426021525     90.02142533584905     52.91310136372895
+    145.9979890111186    108.90056891458975      82.0931937585503     59.42554351667557    132.94210808860396     90.87889944704429    135.03299490189625

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/top_hat2.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/unsharp_mask.gif

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diff -r eabdcf6ad900 -r 69e951528a0b test-data/warping_index1_full.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/warping_index1_full.txt Wed Sep 25 16:04:07 2024 +0000

@@ -0,0 +1,1 @@
+33.63863677975145

diff -r eabdcf6ad900 -r 69e951528a0b test-data/warping_index_raw_full.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/warping_index_raw_full.txt Wed Sep 25 16:04:07 2024 +0000

@@ -0,0 +1,1 @@
+66.40622051430596