Update image_labeling and first example of Fractal integration (ref #64)

.gitignore

@@ -13,3 +13,6 @@ monitoring.db
 
 output*
 tmp_data
+LOG_*
+slurm-*.out
+Local_backup

examples/example_uzh_1_well_2x2_sites.sh

@@ -37,22 +37,22 @@ echo
 
 echo 'Add yokogawa_to_zarr task'
 $CMD task add yokogawa_to_zarr zarr zarr well
-$CMD task list
 echo
 
 #echo 'Add replicate_zarr_structure'
 #$CMD task add replicate_zarr_structure zarr zarr plate
-$CMD task list
-echo
+#echo
 
-#echo 'Add illumination_correction'
-#$CMD task add illumination_correction zarr zarr well
-#$CMD task list
+echo 'Add illumination_correction'
+$CMD task add illumination_correction zarr zarr well
 echo
 
 echo 'Add replicate_zarr_structure_mip'
 $CMD task add replicate_zarr_structure_mip zarr zarr plate
-$CMD task list
+echo
+
+echo 'Add image_labeling'
+$CMD task add image_labeling zarr zarr well
 echo
 
 echo 'Add maximum_intensity_projection'
@@ -64,26 +64,29 @@ echo
 
 echo 'Create workflow'
 $CMD workflow new mwe-test wftest create_zarr_structure
-$CMD workflow list mwe-test
 echo
 
 echo 'Add yokogawa_to_zarr task'
 $CMD workflow add-task mwe-test wftest yokogawa_to_zarr
-$CMD workflow list mwe-test
 echo
 
-#echo 'Add illumination_correction'
-#$CMD workflow add-task mwe-test wftest illumination_correction
-#$CMD workflow list mwe-test
-#echo
+echo 'Add illumination_correction'
+$CMD workflow add-task mwe-test wftest illumination_correction
+echo
+
+echo 'Add image_labeling'
+$CMD workflow add-task mwe-test wftest image_labeling
+echo
 
 echo 'Add replicate_zarr_structure_mip'
 $CMD workflow add-task mwe-test wftest replicate_zarr_structure_mip
-$CMD workflow list mwe-test
 echo
 
 echo 'Add maximum_intensity_projection'
 $CMD workflow add-task mwe-test wftest maximum_intensity_projection
+echo
+
+echo 'Final list:'
 $CMD workflow list mwe-test
 echo
 

examples/wf_params_uzh_1_well_2x2_sites.json

@@ -3,7 +3,7 @@
 "dims": [2, 2],
 "coarsening_xy": 2,
 "coarsening_z": 1,
-"num_levels": 4,
+"num_levels": 5,
 "channel_file": "wf_params_uzh_cardiac_channels.json",
 "path_dict_corr": "wf_params_uzh_cardiac_illumination.json"
 }

fractal/dictionary_tasks.py

@@ -11,12 +11,12 @@
 Institute for Biomedical Research and Pelkmans Lab from the University of
 Zurich.
 """
-
 from fractal.tasks.create_zarr_structure import create_zarr_structure
 from fractal.tasks.create_zarr_structure_multifov import (
     create_zarr_structure_multifov,
 )
 from fractal.tasks.illumination_correction import illumination_correction
+from fractal.tasks.image_labeling import image_labeling
 from fractal.tasks.maximum_intensity_projection import (
     maximum_intensity_projection,
 )
@@ -36,3 +36,4 @@
 dict_tasks["maximum_intensity_projection"] = maximum_intensity_projection
 dict_tasks["replicate_zarr_structure"] = replicate_zarr_structure
 dict_tasks["illumination_correction"] = illumination_correction
+dict_tasks["image_labeling"] = image_labeling

fractal/fractal_cmd.py

@@ -459,6 +459,7 @@ def workflow_apply(
     path_dict_channels = params["channel_file"]
     path_dict_corr = params["path_dict_corr"]
     delete_input = params.get("delete_input", False)
+    labeling_channel = params.get("labeling_channel", "A01_C01")
 
     # FIXME validate tasks somewhere?
 
@@ -478,10 +479,27 @@ def workflow_apply(
         exclusive=fractal_config.exclusive,
     )
     htex = define_HighThroughputExecutor(
-        provider=provider, max_workers=fractal_config.max_workers
+        provider=provider,
+        max_workers=fractal_config.max_workers,
+        label="cpu",
     )
+    provider_gpu = define_SlurmProvider(
+        nodes_per_block=fractal_config.nodes_per_block,
+        cores_per_node=fractal_config.cores_per_node,
+        mem_per_node_GB=fractal_config.mem_per_node_GB,
+        partition=fractal_config.partition_gpu,
+        worker_init=fractal_config.worker_init,
+        max_blocks=fractal_config.max_blocks,
+        exclusive=fractal_config.exclusive,
+    )
+    htex_gpu = define_HighThroughputExecutor(
+        provider=provider_gpu,
+        max_workers=fractal_config.max_workers,
+        label="gpu",
+    )
+
     monitoring = define_MonitoringHub(workflow_name=workflow_name)
-    config = Config(executors=[htex], monitoring=monitoring)
+    config = Config(executors=[htex, htex_gpu], monitoring=monitoring)
     # config = Config(executors=[htex])
     parsl.clear()
     parsl.load(config)
@@ -490,7 +508,7 @@ def workflow_apply(
 
     debug(dict_tasks)
 
-    @parsl.python_app
+    @parsl.python_app(executors=["cpu"])
     def collect_intermediate_results(inputs=[]):
         return [x for x in inputs]
 
@@ -507,7 +525,7 @@ def collect_intermediate_results(inputs=[]):
             num_levels=num_levels,
         )
 
-        @parsl.python_app
+        @parsl.python_app(executors=["cpu"])
         def app_create_zarr_structure(**kwargs_):
             os.environ["OPENBLAS_NUM_THREADS"] = OPENBLAS_NUM_THREADS
             import fractal.dictionary_tasks  # noqa: F401
@@ -542,6 +560,7 @@ def app_create_zarr_structure(**kwargs_):
                 "yokogawa_to_zarr and take a global dict of paths."
             )
 
+        executor = "cpu"
         if task == "yokogawa_to_zarr":
             kwargs = dict(
                 in_path=resources_in[0],  # FIXME
@@ -582,8 +601,15 @@ def app_create_zarr_structure(**kwargs_):
                 overwrite=True,
                 # background=background,
             )
+        elif task == "image_labeling":
+            kwargs = dict(
+                chl_list=chl_list,
+                coarsening_xy=coarsening_xy,
+                labeling_channel=labeling_channel,
+            )
+            executor = "gpu"
 
-        @python_app
+        @python_app(executors=[executor])
         def app(zarrurl, **kwargs_):
             os.environ["OPENBLAS_NUM_THREADS"] = OPENBLAS_NUM_THREADS
             import fractal.dictionary_tasks  # noqa: F401

fractal/fractal_config.py

@@ -11,19 +11,19 @@
 Institute for Biomedical Research and Pelkmans Lab from the University of
 Zurich.
 """
-
 # Parameters of parsl.executors.HighThroughputExecutor
-max_workers = 1  # This is the maximum number of workers per block
+max_workers = 2  # This is the maximum number of workers per block
 
 # Parameters of parsl.providers.SlurmProvider
 # Note that worker_init is a command which is included at the beginning of
 # each SLURM submission scripts
 nodes_per_block = 1  # This implies that a block corresponds to a node
-max_blocks = 15  # Maximum number of blocks (=nodes) that parsl can use
+max_blocks = 24  # Maximum number of blocks (=nodes) that parsl can use
 exclusive = False
 cores_per_node = 16
 mem_per_node_GB = 60
 partition = "main"
+partition_gpu = "gpu"
 worker_init = "source /opt/easybuild/software/Anaconda3/2019.07/"
 worker_init += "etc/profile.d/conda.sh\n"
 worker_init += "conda activate fractal"

fractal/parsl_config.py

@@ -11,7 +11,6 @@
 Institute for Biomedical Research and Pelkmans Lab from the University of
 Zurich.
 """
-
 from parsl.addresses import address_by_hostname
 from parsl.channels import LocalChannel
 from parsl.executors import HighThroughputExecutor
@@ -57,17 +56,18 @@ def define_SlurmProvider(
         parallelism=1,
         exclusive=exclusive,
     )
+
     return slurm
 
 
-def define_HighThroughputExecutor(provider=None, max_workers=40):
+def define_HighThroughputExecutor(provider=None, max_workers=40, label="htex"):
 
     htex = HighThroughputExecutor(
-        label="htex",
+        label=label,
         address=address_by_hostname(),
         # worker_debug=True,
         max_workers=max_workers,
-        cores_per_worker=8,
+        cores_per_worker=16,
         provider=provider,
         cpu_affinity="block",
     )

fractal/tasks/image_labeling.py

@@ -256,8 +256,30 @@ def image_labeling(
     parser.add_argument(
         "-z", "--zarrurl", help="zarr url, at the FOV level", required=True
     )
+    parser.add_argument(
+        "-C",
+        "--chl_list",
+        nargs="+",
+        help="list of channel names (e.g. A01_C01)",
+    )
+    parser.add_argument(
+        "-cxy",
+        "--coarsening_xy",
+        default=2,
+        type=int,
+        help="coarsening factor along X and Y (optional, defaults to 2)",
+    )
+    parser.add_argument(
+        "-lc",
+        "--labeling_channel",
+        help="name of channel for labeling (e.g. A01_C01)",
+    )
 
     args = parser.parse_args()
     image_labeling(
         args.zarrurl,
+        coarsening_xy=args.coarsening_xy,
+        chl_list=args.chl_list,
+        labeling_channel=args.labeling_channel,
+        # FIXME: more arguments
     )