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Integrating labeling tasks into fractal (ref #64 #104) and clean up part of the examples folder
1 parent 12deb67 commit 3c1c431

15 files changed

+189
-79
lines changed

‎.gitignore

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@@ -17,3 +17,7 @@ LOG_*
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slurm-*.out
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Local_backup
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mprofile_*.dat
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.nfs*
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nohup
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nohup.out

‎examples/example_uzh_10_well_5x5_sites.sh renamed to ‎examples/UZH_10_well_5x5_sites/example_uzh_10_well_5x5_sites.sh

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@@ -7,11 +7,14 @@ WFPARAMS=wf_params_uzh_10_well_5x5_sites.json
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MWE_DIR=/data/active/fractal/tests
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PATH_OUTPUT=${MWE_DIR}/Temporary_data_UZH_10_well_5x5_sites
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CMD='poetry run python ../fractal/fractal_cmd.py'
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CMD='poetry run python ../../fractal/fractal_cmd.py'
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#echo 'Re-install poetry'
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#poetry install
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date
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echo
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echo 'Clean up'
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rm -rf $PATH_OUTPUT
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mkdir -p $PATH_OUTPUT
@@ -37,61 +40,73 @@ echo
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echo 'Add yokogawa_to_zarr task'
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$CMD task add yokogawa_to_zarr zarr zarr well
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$CMD task list
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echo
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echo 'Add replicate_zarr_structure'
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$CMD task add replicate_zarr_structure zarr zarr plate
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$CMD task list
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echo
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#echo 'Add replicate_zarr_structure'
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#$CMD task add replicate_zarr_structure zarr zarr plate
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#echo
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echo 'Add illumination_correction'
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$CMD task add illumination_correction zarr zarr well
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$CMD task list
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echo
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echo 'Add replicate_zarr_structure_mip'
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$CMD task add replicate_zarr_structure_mip zarr zarr plate
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$CMD task list
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echo
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echo 'Add image_labeling'
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$CMD task add image_labeling zarr zarr well
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echo
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echo 'Add image_labeling_whole_well'
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$CMD task add image_labeling_whole_well zarr zarr well
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echo
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echo 'Add maximum_intensity_projection'
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$CMD task add maximum_intensity_projection zarr zarr well
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echo
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echo
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$CMD task list
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echo
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#############################################
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echo 'Create workflow'
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$CMD workflow new mwe-test wftest create_zarr_structure
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$CMD workflow list mwe-test
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echo
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echo 'Add yokogawa_to_zarr task'
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$CMD workflow add-task mwe-test wftest yokogawa_to_zarr
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$CMD workflow list mwe-test
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echo
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#echo 'Add replicate_zarr_structure'
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#$CMD workflow add-task mwe-test wftest replicate_zarr_structure
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#$CMD workflow list mwe-test
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#echo
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echo 'Add illumination_correction'
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$CMD workflow add-task mwe-test wftest illumination_correction
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$CMD workflow list mwe-test
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echo
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echo 'Add image_labeling'
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$CMD workflow add-task mwe-test wftest image_labeling
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echo
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echo 'Add replicate_zarr_structure_mip'
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$CMD workflow add-task mwe-test wftest replicate_zarr_structure_mip
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$CMD workflow list mwe-test
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echo
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echo 'Add maximum_intensity_projection'
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$CMD workflow add-task mwe-test wftest maximum_intensity_projection
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echo
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echo 'Add image_labeling_whole_well'
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$CMD workflow add-task mwe-test wftest image_labeling_whole_well
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echo
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echo 'Final list:'
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$CMD workflow list mwe-test
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echo
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echo 'Execute workflow'
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$CMD workflow apply mwe-test wftest dstest dstest $PATH_INPUT $PATH_OUTPUT $WFPARAMS
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echo
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echo
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date

‎examples/UZH_10_well_5x5_sites/wf_params_uzh_10_well_5x5_sites.json

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{
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"workflow_name": "uzh_10_well_5x5_sites",
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"dims": [5, 5],
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"coarsening_xy": 2,
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"coarsening_z": 1,
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"num_levels": 5,
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"channel_file": "../wf_params_uzh_cardiac_channels.json",
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"path_dict_corr": "../wf_params_uzh_cardiac_illumination.json",
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"image_labeling": {"coarsening_xy": 2, "labeling_level": 0, "labeling_channel": "A01_C01", "num_threads": 2, "relabeling": 1, "anisotropy": 6.1538, "diameter": 35.0, "cellprob_threshold": 0.0},
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"image_labeling_whole_well": {"coarsening_xy": 2, "labeling_level": 2, "labeling_channel": "A01_C01", "diameter_level0": 35.0, "cellprob_threshold": 0.0}
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}

‎examples/example_uzh_1_well_2x2_sites.sh renamed to ‎examples/UZH_1_well_2x2_sites/example_uzh_1_well_2x2_sites.sh

Lines changed: 19 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,13 +5,16 @@ PATH_INPUT=/data/active/fractal/3D/PelkmansLab/CardiacMultiplexing/Cycle1_testSu
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WFPARAMS=wf_params_uzh_1_well_2x2_sites.json
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MWE_DIR=/data/active/fractal/tests
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PATH_OUTPUT=${MWE_DIR}/Temporary_data_UZH_1_well_2x2_sites_singlefov
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PATH_OUTPUT=${MWE_DIR}/Temporary_data_UZH_1_well_2x2_sites
99

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CMD='poetry run python ../fractal/fractal_cmd.py'
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CMD='poetry run python ../../fractal/fractal_cmd.py'
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#echo 'Re-install poetry'
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#poetry install
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date
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echo
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echo 'Clean up'
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rm -rf $PATH_OUTPUT
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mkdir -p $PATH_OUTPUT
@@ -55,8 +58,15 @@ echo 'Add image_labeling'
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$CMD task add image_labeling zarr zarr well
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echo
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echo 'Add image_labeling_whole_well'
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$CMD task add image_labeling_whole_well zarr zarr well
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echo
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echo 'Add maximum_intensity_projection'
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$CMD task add maximum_intensity_projection zarr zarr well
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echo
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echo
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$CMD task list
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echo
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@@ -86,10 +96,17 @@ echo 'Add maximum_intensity_projection'
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$CMD workflow add-task mwe-test wftest maximum_intensity_projection
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echo
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echo 'Add image_labeling_whole_well'
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$CMD workflow add-task mwe-test wftest image_labeling_whole_well
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echo
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echo 'Final list:'
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$CMD workflow list mwe-test
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echo
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echo 'Execute workflow'
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$CMD workflow apply mwe-test wftest dstest dstest $PATH_INPUT $PATH_OUTPUT $WFPARAMS
95109
echo
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echo
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date

‎examples/UZH_1_well_2x2_sites/wf_params_uzh_1_well_2x2_sites.json

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{
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"workflow_name": "uzh_1_well_2x2_sites",
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"dims": [2, 2],
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"coarsening_xy": 2,
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"coarsening_z": 1,
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"num_levels": 5,
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"channel_file": "../wf_params_uzh_cardiac_channels.json",
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"path_dict_corr": "../wf_params_uzh_cardiac_illumination.json",
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"image_labeling": {"coarsening_xy": 2, "labeling_level": 0, "labeling_channel": "A01_C01", "num_threads": 2, "relabeling": 1, "anisotropy": 6.1538, "diameter": 35.0, "cellprob_threshold": 0.0},
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"image_labeling_whole_well": {"coarsening_xy": 2, "labeling_level": 2, "labeling_channel": "A01_C01", "diameter_level0": 35.0, "cellprob_threshold": 0.0}
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}

‎examples/example_uzh_1_well_9x8_sites.sh renamed to ‎examples/UZH_1_well_9x8_sites/example_uzh_1_well_9x8_sites.sh

Lines changed: 18 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,11 +7,14 @@ WFPARAMS=wf_params_uzh_1_well_9x8_sites.json
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MWE_DIR=/data/active/fractal/tests
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PATH_OUTPUT=${MWE_DIR}/Temporary_data_UZH_1_well_9x8_sites_singlefov
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CMD='poetry run python ../fractal/fractal_cmd.py'
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CMD='poetry run python ../../fractal/fractal_cmd.py'
1111

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#echo 'Re-install poetry'
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#poetry install
1414

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date
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echo
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echo 'Clean up'
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rm -rf $PATH_OUTPUT
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mkdir -p $PATH_OUTPUT
@@ -55,8 +58,15 @@ echo 'Add image_labeling'
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$CMD task add image_labeling zarr zarr well
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echo
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echo 'Add image_labeling_whole_well'
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$CMD task add image_labeling_whole_well zarr zarr well
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echo
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echo 'Add maximum_intensity_projection'
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$CMD task add maximum_intensity_projection zarr zarr well
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echo
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echo
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$CMD task list
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echo
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@@ -86,10 +96,17 @@ echo 'Add maximum_intensity_projection'
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$CMD workflow add-task mwe-test wftest maximum_intensity_projection
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echo
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echo 'Add image_labeling_whole_well'
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$CMD workflow add-task mwe-test wftest image_labeling_whole_well
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echo
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echo 'Final list:'
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$CMD workflow list mwe-test
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echo
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echo 'Execute workflow'
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$CMD workflow apply mwe-test wftest dstest dstest $PATH_INPUT $PATH_OUTPUT $WFPARAMS
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echo
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echo
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date

‎examples/UZH_1_well_9x8_sites/wf_params_uzh_1_well_9x8_sites.json

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@@ -0,0 +1,11 @@
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{
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"workflow_name": "uzh_1_well_9x8_sites",
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"dims": [9, 8],
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"coarsening_xy": 2,
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"coarsening_z": 1,
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"num_levels": 5,
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"channel_file": "../wf_params_uzh_cardiac_channels.json",
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"path_dict_corr": "../wf_params_uzh_cardiac_illumination.json",
9+
"image_labeling": {"coarsening_xy": 2, "labeling_level": 0, "labeling_channel": "A01_C01", "num_threads": 2, "relabeling": 1, "anisotropy": 6.1538, "diameter": 35.0, "cellprob_threshold": 0.0},
10+
"image_labeling_whole_well": {"coarsening_xy": 2, "labeling_level": 2, "labeling_channel": "A01_C01", "diameter_level0": 35.0, "cellprob_threshold": 0.0}
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}

‎examples/example_uzh_4_well_2x2_sites.sh renamed to ‎examples/UZH_4_well_2x2_sites/example_uzh_4_well_2x2_sites.sh

Lines changed: 32 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -7,11 +7,14 @@ WFPARAMS=wf_params_uzh_4_well_2x2_sites.json
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MWE_DIR=/data/active/fractal/tests
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PATH_OUTPUT=${MWE_DIR}/Temporary_data_UZH_4_well_2x2_sites
99

10-
CMD='poetry run python ../fractal/fractal_cmd.py'
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CMD='poetry run python ../../fractal/fractal_cmd.py'
1111

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#echo 'Re-install poetry'
1313
#poetry install
1414

15+
date
16+
echo
17+
1518
echo 'Clean up'
1619
rm -rf $PATH_OUTPUT
1720
mkdir -p $PATH_OUTPUT
@@ -37,61 +40,73 @@ echo
3740

3841
echo 'Add yokogawa_to_zarr task'
3942
$CMD task add yokogawa_to_zarr zarr zarr well
40-
$CMD task list
4143
echo
4244

43-
echo 'Add replicate_zarr_structure'
44-
$CMD task add replicate_zarr_structure zarr zarr plate
45-
$CMD task list
46-
echo
45+
#echo 'Add replicate_zarr_structure'
46+
#$CMD task add replicate_zarr_structure zarr zarr plate
47+
#echo
4748

4849
echo 'Add illumination_correction'
4950
$CMD task add illumination_correction zarr zarr well
50-
$CMD task list
5151
echo
5252

5353
echo 'Add replicate_zarr_structure_mip'
5454
$CMD task add replicate_zarr_structure_mip zarr zarr plate
55-
$CMD task list
55+
echo
56+
57+
echo 'Add image_labeling'
58+
$CMD task add image_labeling zarr zarr well
59+
echo
60+
61+
echo 'Add image_labeling_whole_well'
62+
$CMD task add image_labeling_whole_well zarr zarr well
5663
echo
5764

5865
echo 'Add maximum_intensity_projection'
5966
$CMD task add maximum_intensity_projection zarr zarr well
67+
echo
68+
69+
echo
6070
$CMD task list
6171
echo
6272

6373
#############################################
6474

6575
echo 'Create workflow'
6676
$CMD workflow new mwe-test wftest create_zarr_structure
67-
$CMD workflow list mwe-test
6877
echo
6978

7079
echo 'Add yokogawa_to_zarr task'
7180
$CMD workflow add-task mwe-test wftest yokogawa_to_zarr
72-
$CMD workflow list mwe-test
7381
echo
7482

75-
#echo 'Add replicate_zarr_structure'
76-
#$CMD workflow add-task mwe-test wftest replicate_zarr_structure
77-
#$CMD workflow list mwe-test
78-
#echo
79-
8083
echo 'Add illumination_correction'
8184
$CMD workflow add-task mwe-test wftest illumination_correction
82-
$CMD workflow list mwe-test
85+
echo
86+
87+
echo 'Add image_labeling'
88+
$CMD workflow add-task mwe-test wftest image_labeling
8389
echo
8490

8591
echo 'Add replicate_zarr_structure_mip'
8692
$CMD workflow add-task mwe-test wftest replicate_zarr_structure_mip
87-
$CMD workflow list mwe-test
8893
echo
8994

9095
echo 'Add maximum_intensity_projection'
9196
$CMD workflow add-task mwe-test wftest maximum_intensity_projection
97+
echo
98+
99+
echo 'Add image_labeling_whole_well'
100+
$CMD workflow add-task mwe-test wftest image_labeling_whole_well
101+
echo
102+
103+
echo 'Final list:'
92104
$CMD workflow list mwe-test
93105
echo
94106

95107
echo 'Execute workflow'
96108
$CMD workflow apply mwe-test wftest dstest dstest $PATH_INPUT $PATH_OUTPUT $WFPARAMS
97109
echo
110+
111+
echo
112+
date

‎examples/UZH_4_well_2x2_sites/wf_params_uzh_4_well_2x2_sites.json

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1+
{
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"workflow_name": "uzh_4_well_2x2_sites",
3+
"dims": [2, 2],
4+
"coarsening_xy": 2,
5+
"coarsening_z": 1,
6+
"num_levels": 5,
7+
"channel_file": "../wf_params_uzh_cardiac_channels.json",
8+
"path_dict_corr": "../wf_params_uzh_cardiac_illumination.json",
9+
"image_labeling": {"coarsening_xy": 2, "labeling_level": 0, "labeling_channel": "A01_C01", "num_threads": 1, "relabeling": 1, "anisotropy": 6.1538, "diameter": 35.0, "cellprob_threshold": 0.0},
10+
"image_labeling_whole_well": {"coarsening_xy": 2, "labeling_level": 2, "labeling_channel": "A01_C01", "diameter_level0": 35.0, "cellprob_threshold": 0.0}
11+
}

‎examples/wf_params_uzh_1_well_2x2_sites.json

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This file was deleted.

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