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Add working 2D example
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‎examples/14_2D_only_test/README.md

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**IMPORTANT**: The `BASE_FOLDER_EXAMPLE` at the top of the script needs to be adapted to point to the examples folder of the user you submit the example from.
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This example ran successfully with:
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* `fractal-server==0.3.5, fractal-client==0.2.9, fracal-tasks-core==0.2.6`
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The features were not calculated yet and couldn't find the issue on first tests. Let's revisit in server 1.x version with the better logs

‎examples/14_2D_only_test/aux_extract_id_from_project_json.py

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import json
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import sys
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msg = (
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"Usage 1: python aux_extract_id_from_project_json.py FILENAME"
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"project_id\nUsage 2: python aux_extract_id_from_project_json.py"
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" FILENAME dataset_id DATASET_NAME"
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)
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if len(sys.argv[1:]) < 2:
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raise Exception(msg)
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filename, which_id = sys.argv[1:3]
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if which_id == "dataset_id":
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if len(sys.argv[1:]) != 3:
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raise Exception(msg)
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dataset_name = sys.argv[3]
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with open(filename, "r") as fin:
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d = json.load(fin)
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if which_id == "project_id":
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# Safety check
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print(d["id"])
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elif which_id == "dataset_id":
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dataset_list = d["dataset_list"]
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dataset_id = next(
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ds["id"] for ds in dataset_list if ds["name"] == dataset_name
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)
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print(dataset_id)
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else:
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raise Exception("ERROR: {which_id=}")

‎examples/14_2D_only_test/regionprops_from_existing_labels_feature.yaml

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!!python/object:napari_workflows._workflow.Workflow
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_tasks:
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regionprops_DAPI: !!python/tuple
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- !!python/name:napari_skimage_regionprops._regionprops.regionprops_table ''
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- dapi_img
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- label_img
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- true
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- true
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- false
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- false
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- false
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- false

‎examples/14_2D_only_test/run_example.sh

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# For the demo: Run everything as the current user
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USERNAME="$(whoami)"
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PORT=8001
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echo -e "FRACTAL_USER=$USERNAME@me.com\nFRACTAL_PASSWORD=test\nFRACTAL_SERVER=http://localhost:$PORT" > .fractal.env
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###############################################################################
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# THINGS TO BE CHANGED BY THE USER
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# Adapt to settings to where you run the example
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BASE_FOLDER_EXAMPLE="/data/homes/$USERNAME/03_fractal/fractal-demos/examples"
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###############################################################################
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LABEL="2d_only"
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###############################################################################
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# IMPORTANT: modify the following lines, depending on your preferences
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# 1. They MUST include a `cd` command to a path where your user can write. The
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# simplest is to use `cd $HOME`, but notice that this will create many sh
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# scripts in your folder. You can also use `cd $HOME/.fractal_scripts`, but
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# first make sure that such folder exists
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# 2. They MAY include additional commands to load a python environment. The ones
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# used in the current example are appropriate for the UZH Pelkmans lab setup.
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TARGET_DIR=~/.tmp_fractal
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rm -r $TARGET_DIR
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mkdir $TARGET_DIR
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WORKER_INIT="\
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export HOME=$HOME; \
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cd $TARGET_DIR; \
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source /opt/easybuild/software/Anaconda3/2019.07/etc/profile.d/conda.sh; \
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conda activate /data/homes/fractal/sharedfractal; \
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"
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###############################################################################
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# Set useful variables
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PRJ_NAME="2proj-"$USERNAME
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DS_IN_NAME="input-ds-"$USERNAME
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DS_OUT_NAME="output-ds-"$USERNAME
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WF_NAME="2WF-2x2-"$USERNAME
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# Set cache path and remove any previous file from there
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export FRACTAL_CACHE_PATH=`pwd`/".cache"
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rm -v ${FRACTAL_CACHE_PATH}/session
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rm -v ${FRACTAL_CACHE_PATH}/tasks
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# Define/initialize empty project folder and temporary file
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PROJ_DIR=$BASE_FOLDER_EXAMPLE/tmp_${LABEL}
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rm -r $PROJ_DIR
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mkdir $PROJ_DIR
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TMPJSON=${PROJ_DIR}/tmp.json
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###############################################################################
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# IMPORTANT: modify the following lines so that they point to absolute paths
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INPUT_PATH="/data/active/fractal/2D/hiPSC_Slice/2D_test_set"
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OUTPUT_PATH='/data/active/jluethi/Fractal/20221110-2D-only-test/'
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###############################################################################
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# Define useful auxiliary command (this will be removed in the future)
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CMD_JSON="python aux_extract_id_from_project_json.py $TMPJSON"
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# Create project
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fractal -j project new $PRJ_NAME $PROJ_DIR > $TMPJSON
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PRJ_ID=`$CMD_JSON project_id`
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DS_IN_ID=`$CMD_JSON dataset_id "default"`
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echo "PRJ_ID: $PRJ_ID"
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echo "DS_IN_ID: $DS_IN_ID"
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# Update dataset name/type, and add a resource
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fractal dataset edit --name "$DS_IN_NAME" -t image --read-only $PRJ_ID $DS_IN_ID
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fractal dataset add-resource -g "*.png" $PRJ_ID $DS_IN_ID $INPUT_PATH
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# Add output dataset, and add a resource to it
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DS_OUT_ID=`fractal --batch project add-dataset $PRJ_ID "$DS_OUT_NAME"`
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fractal dataset edit -t zarr --read-write $PRJ_ID $DS_OUT_ID
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fractal dataset add-resource -g "*.zarr" $PRJ_ID $DS_OUT_ID $OUTPUT_PATH
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# Create workflow
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WF_ID=`fractal --batch task new "$WF_NAME" workflow image zarr`
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echo "WF_ID: $WF_ID"
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# Add subtasks
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echo "{\"num_levels\": 5, \"executor\": \"cpu-low\", \"coarsening_xy\": 2, \"channel_parameters\": {\"A01_C01\": {\"label\": \"Channel 1\",\"colormap\": \"00FFFF\",\"start\": 110,\"end\": 700 }, \"A01_C02\": {\"label\": \"Channel 2\",\"colormap\": \"FF00FF\",\"start\": 110,\"end\": 1500 }, \"A02_C03\": {\"label\": \"Channel 3\",\"colormap\": \"FFFF00\",\"start\": 110,\"end\": 1500 }}}" > ${PROJ_DIR}/args_create.json
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fractal task add-subtask $WF_ID "Create OME-ZARR structure" --args-file ${PROJ_DIR}/args_create.json
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echo "{\"executor\": \"cpu-mid\"}" > ${PROJ_DIR}/args_yoko.json
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fractal task add-subtask $WF_ID "Yokogawa to Zarr" > ${PROJ_DIR}/args_yoko.json
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# # Paths of illumination correction images need to be accessible on the server.
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# # This works if one runs the client from the same machine as the server. Otherwise, change `root_path_corr`
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# echo "{\"overwrite\": true, \"executor\": \"cpu-low\", \"dict_corr\": {\"root_path_corr\": \"$BASE_FOLDER_EXAMPLE/../demo-october-2022/illum_corr_images/\", \"A01_C01\": \"20220621_UZH_manual_illumcorr_40x_A01_C01.png\", \"A01_C02\": \"20220621_UZH_manual_illumcorr_40x_A01_C02.png\", \"A02_C03\": \"20220621_UZH_manual_illumcorr_40x_A02_C03.png\"}}" > ${PROJ_DIR}/args_illum.json
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# fractal task add-subtask $WF_ID "Illumination correction" --args-file ${PROJ_DIR}/args_illum.json
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# Doing an MIP on a 2D dataset isn't meaningful.
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# Included here in the test to check that it doesn't mess anything up. It's fine in my tests
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echo "{\"executor\": \"cpu-low\"}" > ${PROJ_DIR}/args_replicate.json
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fractal task add-subtask $WF_ID "Replicate Zarr structure" --args-file ${PROJ_DIR}/args_replicate.json
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echo "{\"executor\": \"cpu-low\"}" > ${PROJ_DIR}/args_mip.json
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fractal task add-subtask $WF_ID "Maximum Intensity Projection" --args-file ${PROJ_DIR}/args_mip.json
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echo "{\"labeling_level\": 2, \"executor\": \"cpu-low\", \"ROI_table_name\": \"well_ROI_table\"}" > ${PROJ_DIR}/args_labeling.json
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fractal task add-subtask $WF_ID "Cellpose Segmentation" --args-file ${PROJ_DIR}/args_labeling.json
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echo "{\"level\": 0, \"measurement_table_name\": \"nuclei\", \"executor\": \"cpu-mid\", \"ROI_table_name\": \"well_ROI_table\",\"workflow_file\": \"$BASE_FOLDER_EXAMPLE/14_2D_only_test/regionprops_from_existing_labels_feature.yaml\"}" > ${PROJ_DIR}/args_measurement.json
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fractal task add-subtask $WF_ID "Measurement" --args-file ${PROJ_DIR}/args_measurement.json
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# Apply workflow
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fractal task apply $PRJ_ID $DS_IN_ID $DS_OUT_ID $WF_ID --worker_init "$WORKER_INIT"

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