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Fix TypeError when getOverlay() returns None with no particles (bgruening#1886)
* Fix TypeError when getOverlay() returns None with no particles * Bump VERSION_SUFFIX to 1 * Fix confocal-series-first-channel.tif typo in test data * Fix conditional parameter values in test cases * Fix expected test data for no-particles-match test case The new size=100000-Infinity test on blobs.gif matches zero particles, so the results table is empty. It incorrectly reused analyze_particles_nothing.tabular, which is shared by two other tests (show=Nothing and Overlay_Masks) that DO match all 63 blobs. Instead of breaking those, assert the results output has 0 lines. Also add the trailing newline to analyze_particles_rois_empty.tabular to match the header written by the jython script (which ends with \n). --------- Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
1 parent dd275a3 commit 6b07980

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Lines changed: 69 additions & 26 deletions

‎tools/image_processing/imagej2/imagej2_adjust_threshold_binary.xml‎

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@@ -126,7 +126,7 @@ $method_cond.threshold_max
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<output name="output" file="blobs_threshold_0-8.gif" compare="image_diff" metric="iou"/>
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</test>
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<test>
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<param name="input" value="confocal-series-first-channel.tif"/>
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<param name="input" value="confocal-series-first-channel.tiff"/>
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<conditional name="method_cond">
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<param name="method" value="Default"/>
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<param name="black_background" value="yes"/>

‎tools/image_processing/imagej2/imagej2_analyze_particles_binary.xml‎

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<output name="results" file="confocal_analyze_particles.tabular"/>
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<output name="rois" file="confocal_analyze_particles_rois.tabular"/>
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</test>
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<test expect_num_outputs="2">
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<param name="input" value="blobs.gif"/>
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<param name="size" value="100000-Infinity"/>
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<param name="show" value="Nothing"/>
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<param name="export_rois" value="true"/>
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<output name="results">
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<assert_contents>
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<has_n_lines n="0"/>
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</assert_contents>
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</output>
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<output name="rois" file="analyze_particles_rois_empty.tabular"/>
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</test>
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</tests>
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<help>
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.. class:: warningmark

‎tools/image_processing/imagej2/imagej2_analyze_particles_binary_jython_script.py‎

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@@ -60,7 +60,7 @@
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options2 = list(options)
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options2.append("show=Overlay")
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IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options2))
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ov = input_image_plus_copy.getOverlay()
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ov = input_image_plus_copy.getOverlay() or []
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with open(roi_coordinate_file, 'w') as fo:
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fo.write("shape\tpoints\tlabel\tt\tz\n")
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for i, roi in enumerate(ov):

‎tools/image_processing/imagej2/imagej2_bunwarpj_align.xml‎

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<!-- Align two images without landmarks or mask, but saving transformation matrices -->
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<expand macro="test_target_source_images"/>
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<param name="max_subsamp_fact" value="1"/>
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<param name="advanced_options" value="save_transformation"/>
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<conditional name="advanced_options_cond">
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<param name="advanced_options" value="save_transformation"/>
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</conditional>
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<output name="source_out" file="registered_source1_forced1cpu.png" compare="image_diff"/>
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<output name="target_out" file="registered_target1_forced1cpu.png" compare="image_diff"/>
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<output name="source_trans_out" file="source_elastic_transformation_out.txt" compare="contains"/>
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<test expect_num_outputs="2">
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<!-- Align two images without landmarks but with mask, not saving transformation matrices -->
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<expand macro="test_target_source_images"/>
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<param name="align_with_mask" value="yes"/>
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<param name="target_mask" value="mask_white.png"/>
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<param name="source_mask" value="mask_ramp.gif"/>
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<conditional name="align_with_mask_cond">
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<param name="align_with_mask" value="yes"/>
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<param name="target_mask" value="mask_white.png"/>
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<param name="source_mask" value="mask_ramp.gif"/>
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</conditional>
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<param name="max_subsamp_fact" value="1"/>
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<output name="source_out" file="registered_source2_forced1cpu.png" compare="image_diff"/>
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<output name="target_out" file="registered_target2_forced1cpu.png" compare="image_diff"/>

‎tools/image_processing/imagej2/imagej2_enhance_contrast.xml‎

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@@ -58,18 +58,26 @@ ImageJ --ij2 --headless --debug
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<tests>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="equalize_histogram" value="yes"/>
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<conditional name="equalize_histogram_cond">
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<param name="equalize_histogram" value="yes"/>
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</conditional>
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<output name="output" file="blobs_equalize.gif" compare="image_diff"/>
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</test>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="saturated_pixels" value="6.2"/>
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<conditional name="equalize_histogram_cond">
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<param name="equalize_histogram" value="no"/>
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<param name="saturated_pixels" value="6.2"/>
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</conditional>
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<output name="output" file="blobs_saturate.gif" compare="image_diff"/>
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</test>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="saturated_pixels" value="13.0"/>
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<param name="normalize" value="yes"/>
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<conditional name="equalize_histogram_cond">
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<param name="equalize_histogram" value="no"/>
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<param name="saturated_pixels" value="13.0"/>
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<param name="normalize" value="yes"/>
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</conditional>
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<output name="output" file="blobs_normalize.gif" compare="image_diff"/>
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</test>
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</tests>

‎tools/image_processing/imagej2/imagej2_macros.xml‎

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<macros>
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<token name="@TOOL_VERSION@">20240614</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<token name="@VERSION_SUFFIX@">1</token>
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<xml name="fiji_requirements">
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">fiji</requirement>

‎tools/image_processing/imagej2/imagej2_math.xml‎

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<tests>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="operation" value="Multiply"/>
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<conditional name="operation_cond">
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<param name="operation" value="Multiply"/>
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</conditional>
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<output name="output" file="blobs_multiply.gif" compare="image_diff"/>
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</test>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="operation" value="Min"/>
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<param name="float_constant" value="255"/>
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<conditional name="operation_cond">
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<param name="operation" value="Min"/>
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<param name="float_constant" value="255"/>
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</conditional>
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<output name="output" file="blobs_min.gif" compare="image_diff"/>
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</test>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="operation" value="Log"/>
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<conditional name="operation_cond">
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<param name="operation" value="Log"/>
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</conditional>
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<output name="output" file="blobs_log.gif" compare="image_diff"/>
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</test>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="operation" value="Square"/>
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<conditional name="operation_cond">
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<param name="operation" value="Square"/>
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</conditional>
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<output name="output" file="blobs_square.gif" compare="image_diff"/>
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</test>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="operation" value="Macro"/>
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<conditional name="operation_cond">
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<param name="operation" value="Macro"/>
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</conditional>
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<output name="output" file="blobs_macro.gif" compare="image_diff"/>
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</test>
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</tests>

‎tools/image_processing/imagej2/imagej2_noise.xml‎

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<tests>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="noise" value="add_specified_noise"/>
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<param name="standard_deviation" value="5" />
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<conditional name="noise_cond">
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<param name="noise" value="add_specified_noise"/>
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<param name="standard_deviation" value="5"/>
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</conditional>
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<!-- Cannot use image_diff as the noise is random -->
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<output name="output" file="add_specified_noise.gif" compare="sim_size"/>
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</test>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="noise" value="despeckle"/>
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<conditional name="noise_cond">
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<param name="noise" value="despeckle"/>
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</conditional>
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<output name="output" file="despeckle.gif" compare="image_diff"/>
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</test>
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<test>
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<param name="input" value="blobs.gif"/>
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<param name="noise" value="remove_outliers"/>
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<param name="radius" value="10.0"/>
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<param name="threshold" value="1"/>
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<param name="which_outliers" value="Bright"/>
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<conditional name="noise_cond">
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<param name="noise" value="remove_outliers"/>
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<param name="radius" value="10.0"/>
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<param name="threshold" value="1"/>
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<param name="which_outliers" value="Bright"/>
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</conditional>
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<output name="output" file="remove_outliers.gif" compare="image_diff"/>
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</test>
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<test expect_failure="true">
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<param name="input" value="blobs.gif"/>
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<param name="noise" value="remove_nans"/>
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<conditional name="noise_cond">
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<param name="noise" value="remove_nans"/>
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</conditional>
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</test>
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</tests>
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<help>

‎tools/image_processing/imagej2/test-data/analyze_particles_rois_empty.tabular‎

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shape points label t z

‎tools/image_processing/imagej2/test-data/regenerate_outputs.sh‎

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# Test 5
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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'
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# Test 6
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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'
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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.tiff' 0.0 255.0 'Default' 'bw' 'yes' 'tools/image_processing/imagej2/test-data/confocal-series-first-channel_threshold_default.tiff' 'tiff'
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# Analyze particles

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