Mercurial > repos > imgteam > superdsm
changeset 2:244f67290d28 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
| author | imgteam |
|---|---|
| date | Mon, 13 Nov 2023 22:12:35 +0000 |
| parents | 700ae37e5c69 |
| children | 7fd8dba15bd3 |
| files | run-superdsm.py superdsm.xml |
| diffstat | 2 files changed, 75 insertions(+), 64 deletions(-) [+] |
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--- a/run-superdsm.py Thu Jul 06 00:01:18 2023 +0000 +++ b/run-superdsm.py Mon Nov 13 22:12:35 2023 +0000 @@ -13,11 +13,6 @@ import shutil import tempfile -import ray -import superdsm.automation -import superdsm.io -import superdsm.render - hyperparameters = [ ('AF_scale', float), @@ -71,7 +66,11 @@ os.environ['MKL_NUM_THREADS'] = str(num_threads_per_process) os.environ['OPENBLAS_NUM_THREADS'] = str(num_threads_per_process) - os.environ['MKL_DEBUG_CPU_TYPE'] = '5' + + import ray + import superdsm.automation + import superdsm.io + import superdsm.render ray.init(num_cpus=num_processes, log_to_driver=True)
--- a/superdsm.xml Thu Jul 06 00:01:18 2023 +0000 +++ b/superdsm.xml Mon Nov 13 22:12:35 2023 +0000 @@ -1,64 +1,76 @@ -<tool id="ip_superdsm" name="SuperDSM" version="0.1.3" profile="20.05"> - <description>globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</description> - <requirements> +<tool id="ip_superdsm" name="Perform segmentation using deformable shape models" version="0.1.3+galaxy2" profile="20.05"> + <description>with SuperDSM</description> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="bio.tools">superdsm</xref> + <xref type="biii">superdsm</xref> + </xrefs> + <requirements> <requirement type="package" version="0.1.3">superdsm</requirement> <requirement type="package" version="1.6.0">ray-core</requirement> <requirement type="package" version="0.18.1">scikit-image</requirement> - </requirements> - <command detect_errors="aggressive"> - <![CDATA[ - python '$__tool_directory__/run-superdsm.py' - '${dataset}' - 'cfg.json' - 'masks.png' - 'overlay.png' - $seg_border - \${GALAXY_SLOTS:-4} - #if str($config.AF_scale) != '': - --AF_scale '${config.AF_scale}' - #end if - #if str($config.c2f_region_analysis_min_atom_radius) != '': - --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}' - #end if - #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '': - --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}' - #end if - #if str($config.c2f_region_analysis_max_atom_norm_energy) != '': - --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}' - #end if - #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '': - --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}' - #end if - #if str($config.dsm_alpha) != '': - --dsm_alpha '${config.dsm_alpha}' - #end if - #if str($config.dsm_AF_alpha) != '': - --dsm_AF_alpha '${config.dsm_AF_alpha}' - #end if - #if str($config.global_energy_minimization_beta) != '': - --global_energy_minimization_beta '${config.global_energy_minimization_beta}' - #end if - #if str($config.global_energy_minimization_AF_beta) != '': - --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}' - #end if - #if str($config.postprocess_mask_max_distance) != '': - --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}' - #end if - #if str($config.postprocess_mask_stdamp) != '': - --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}' - #end if - #if str($config.postprocess_max_norm_energy) != '': - --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}' - #end if - #if str($config.postprocess_min_contrast) != '': - --postprocess_min_contrast '${config.postprocess_min_contrast}' - #end if - #if str($config.postprocess_min_object_radius) != '': - --postprocess_min_object_radius '${config.postprocess_min_object_radius}' - #end if - ]]> - </command> - <inputs> + <requirement type="package" version="2020.0">mkl</requirement><!-- this seems to be the last version of MKL which supports the "MKL_DEBUG_CPU_TYPE" environment variable --> + <requirement type="package" version="*=mkl">blas</requirement><!-- using MKL instead of other BLAS can significantly improve performance on some hardware, cf. https://stackoverflow.com/questions/62783262/why-is-numpy-with-ryzen-threadripper-so-much-slower-than-xeon --> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + python '$__tool_directory__/run-superdsm.py' + '${dataset}' + 'cfg.json' + 'masks.png' + 'overlay.png' + $seg_border + \${GALAXY_SLOTS:-4} + #if str($config.AF_scale) != '': + --AF_scale '${config.AF_scale}' + #end if + #if str($config.c2f_region_analysis_min_atom_radius) != '': + --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}' + #end if + #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '': + --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}' + #end if + #if str($config.c2f_region_analysis_max_atom_norm_energy) != '': + --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}' + #end if + #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '': + --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}' + #end if + #if str($config.dsm_alpha) != '': + --dsm_alpha '${config.dsm_alpha}' + #end if + #if str($config.dsm_AF_alpha) != '': + --dsm_AF_alpha '${config.dsm_AF_alpha}' + #end if + #if str($config.global_energy_minimization_beta) != '': + --global_energy_minimization_beta '${config.global_energy_minimization_beta}' + #end if + #if str($config.global_energy_minimization_AF_beta) != '': + --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}' + #end if + #if str($config.postprocess_mask_max_distance) != '': + --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}' + #end if + #if str($config.postprocess_mask_stdamp) != '': + --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}' + #end if + #if str($config.postprocess_max_norm_energy) != '': + --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}' + #end if + #if str($config.postprocess_min_contrast) != '': + --postprocess_min_contrast '${config.postprocess_min_contrast}' + #end if + #if str($config.postprocess_min_object_radius) != '': + --postprocess_min_object_radius '${config.postprocess_min_object_radius}' + #end if + ]]> + </command> + <environment_variables> + <environment_variable name="MKL_DEBUG_CPU_TYPE">5</environment_variable><!-- this enables accelerated CPU instruction sets on AMD hardware, does nothing in Intel hardware, thus no need to change this --> + </environment_variables> + <inputs> <param name="dataset" type="data" format="tiff,png" label="Dataset" /> <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels) of the segmentation results (overlays)" /> <section name="config" title="Hyperparameters" expanded="false">