Merge pull request #814 from fractal-analytics-platform/813_projections

Add different projection methods

CHANGELOG.md

@@ -1,6 +1,6 @@
 **Note**: Numbers like (\#123) point to closed Pull Requests on the fractal-tasks-core repository.
 
-# Unreleased
+# 1.3.0
 * Tasks:
     * `image_glob_patterns` are renamed to `include_glob_patterns` in Convert Cellvoyager to OME-Zarr (regular & multiplexing) (\#812).
     * Convert Cellvoyager to OME-Zarr (regular & multiplexing) gain exclusion patterns to exclude specific patterns of images from being processed (\#812).
@@ -9,6 +9,9 @@
     * In Convert Cellvoyager to OME-Zarr, improve plate metadata for image list when multiple plates with the same plate name are processed (\#812).
     * Catch errors for missing mlf & mrf files better in Convert Cellvoyager to OME-Zarr (regular & multiplexing) (\#812).
     * Drop defusexml dependency for cellvoyager metadata conversion (\#812).
+    * Rename `Maximum Intensity Projection HCS Plate` task to `Project Image (HCS Plate)` (\#814).
+    * Expose selection of projection modes in `Project Image (HCS Plate)`: MIP, MINIP, MEANIP & SUMIP (\#814).
+    * Rename task function from `maximum_intensity_projection` to `projection` and modified parameters in `fractal_tasks_core.tasks.io_models.InitArgsMIP` (\#814).
 
 # 1.2.1
 * Core-library

examples/02_cardio_tiny_mip/run_workflow.py

@@ -28,8 +28,8 @@
 from fractal_tasks_core.tasks.copy_ome_zarr_hcs_plate import (
     copy_ome_zarr_hcs_plate,
 )
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 
 allowed_channels = [
@@ -98,7 +98,7 @@
 debug(parallelization_list)
 
 for image in parallelization_list["parallelization_list"]:
-    maximum_intensity_projection(
+    projection(
         zarr_url=image["zarr_url"],
         init_args=image["init_args"],
         # overwrite=True,

examples/old/_06_cellpose_dev_example/run_example_cellpose_dual_channel.py

@@ -22,8 +22,8 @@
 )
 from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr
 from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
 
@@ -98,7 +98,7 @@
 
 # Make MIP
 for component in metadata["image"]:
-    metadata_update = maximum_intensity_projection(
+    metadata_update = projection(
         input_paths=[zarr_path],
         output_path=zarr_path,
         metadata=metadata,

examples/old/_06_cellpose_dev_example/run_example_cellpose_normalization.py

@@ -25,8 +25,8 @@
 )
 from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr
 from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
 
@@ -91,7 +91,7 @@
 
 # Make MIP
 for component in metadata["image"]:
-    metadata_update = maximum_intensity_projection(
+    metadata_update = projection(
         input_paths=[zarr_path],
         output_path=zarr_path,
         metadata=metadata,

examples/old/_08_subset_of_data/run_example_single_channel.py

@@ -6,8 +6,8 @@
 from fractal_tasks_core.channels import Window
 from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr
 from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
 
@@ -82,7 +82,7 @@
 
 # Make MIP
 for component in metadata["image"]:
-    metadata_update = maximum_intensity_projection(
+    metadata_update = projection(
         input_paths=[zarr_path],
         output_path=zarr_path,
         metadata=metadata,

examples/old/_08_subset_of_data/run_example_single_channel_few_Z_planes.py

@@ -6,8 +6,8 @@
 from fractal_tasks_core.channels import Window
 from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr
 from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
 
@@ -82,7 +82,7 @@
 
 # Make MIP
 for component in metadata["image"]:
-    metadata_update = maximum_intensity_projection(
+    metadata_update = projection(
         input_paths=[zarr_path],
         output_path=zarr_path,
         metadata=metadata,

examples/old/_08_subset_of_data/run_example_single_channel_single_Z_plane.py

@@ -6,8 +6,8 @@
 from fractal_tasks_core.channels import Window
 from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr
 from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
 
@@ -82,7 +82,7 @@
 
 # Make MIP
 for component in metadata["image"]:
-    metadata_update = maximum_intensity_projection(
+    metadata_update = projection(
         input_paths=[zarr_path],
         output_path=zarr_path,
         metadata=metadata,

examples/old/_08_subset_of_data/run_example_two_channel_two_Z_planes.py

@@ -6,8 +6,8 @@
 from fractal_tasks_core.channels import Window
 from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr
 from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
 
@@ -82,7 +82,7 @@
 
 # Make MIP
 for component in metadata["image"]:
-    metadata_update = maximum_intensity_projection(
+    metadata_update = projection(
         input_paths=[zarr_path],
         output_path=zarr_path,
         metadata=metadata,

examples/old/_08_subset_of_data/run_example_two_channel_two_Z_planes_single_FOV.py

@@ -6,8 +6,8 @@
 from fractal_tasks_core.channels import Window
 from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr
 from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
 
@@ -82,7 +82,7 @@
 
 # Make MIP
 for component in metadata["image"]:
-    metadata_update = maximum_intensity_projection(
+    metadata_update = projection(
         input_paths=[zarr_path],
         output_path=zarr_path,
         metadata=metadata,

examples/old/_09_secondary_labeling/01_images_to_mip.py

@@ -7,8 +7,8 @@
 from fractal_tasks_core.channels import Window
 from fractal_tasks_core.tasks.copy_ome_zarr import copy_ome_zarr
 from fractal_tasks_core.tasks.create_ome_zarr import create_ome_zarr
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.tasks.yokogawa_to_ome_zarr import yokogawa_to_ome_zarr
 
@@ -91,7 +91,7 @@
 
 # MIP
 for component in metadata["image"]:
-    maximum_intensity_projection(
+    projection(
         input_paths=[zarr_path_mip],
         output_path=zarr_path_mip,
         metadata=metadata,

fractal_tasks_core/__FRACTAL_MANIFEST__.json

@@ -544,15 +544,15 @@
       "docs_link": "https://fractal-analytics-platform.github.io/fractal-tasks-core"
     },
     {
-      "name": "Maximum Intensity Projection HCS Plate",
+      "name": "Project Image (HCS Plate)",
       "input_types": {
         "is_3D": true
       },
       "output_types": {
         "is_3D": false
       },
       "executable_non_parallel": "tasks/copy_ome_zarr_hcs_plate.py",
-      "executable_parallel": "tasks/maximum_intensity_projection.py",
+      "executable_parallel": "tasks/projection.py",
       "meta_non_parallel": {
         "cpus_per_task": 1,
         "mem": 4000
@@ -562,6 +562,19 @@
         "mem": 4000
       },
       "args_schema_non_parallel": {
+        "$defs": {
+          "DaskProjectionMethod": {
+            "description": "Registration method selection",
+            "enum": [
+              "mip",
+              "minip",
+              "meanip",
+              "sumip"
+            ],
+            "title": "DaskProjectionMethod",
+            "type": "string"
+          }
+        },
         "additionalProperties": false,
         "properties": {
           "zarr_urls": {
@@ -577,11 +590,15 @@
             "type": "string",
             "description": "path of the directory where the new OME-Zarrs will be created. (standard argument for Fractal tasks, managed by Fractal server)."
           },
-          "suffix": {
+          "method": {
+            "allOf": [
+              {
+                "$ref": "#/$defs/DaskProjectionMethod"
+              }
+            ],
             "default": "mip",
-            "title": "Suffix",
-            "type": "string",
-            "description": "The suffix that is used to transform `plate.zarr` into `plate_suffix.zarr`. Note that `None` is not currently supported."
+            "title": "Method",
+            "description": "Choose which method to use for intensity projection along the Z axis. mip is the default and performs a maximum intensity projection. minip performs a minimum intensity projection, meanip a mean intensity projection and sumip a sum intensity projection."
           },
           "overwrite": {
             "default": false,
@@ -605,10 +622,20 @@
               "origin_url": {
                 "title": "Origin Url",
                 "type": "string"
+              },
+              "method": {
+                "title": "Method",
+                "type": "string"
+              },
+              "overwrite": {
+                "title": "Overwrite",
+                "type": "boolean"
               }
             },
             "required": [
-              "origin_url"
+              "origin_url",
+              "method",
+              "overwrite"
             ],
             "title": "InitArgsMIP",
             "type": "object"
@@ -625,22 +652,16 @@
             "$ref": "#/$defs/InitArgsMIP",
             "title": "Init Args",
             "description": "Intialization arguments provided by `create_cellvoyager_ome_zarr_init`."
-          },
-          "overwrite": {
-            "default": false,
-            "title": "Overwrite",
-            "type": "boolean",
-            "description": "If `True`, overwrite the task output."
           }
         },
         "required": [
           "zarr_url",
           "init_args"
         ],
         "type": "object",
-        "title": "MaximumIntensityProjection"
+        "title": "Projection"
       },
-      "docs_info": "## copy_ome_zarr_hcs_plate\nDuplicate the OME-Zarr HCS structure for a set of zarr_urls.\n\nThis task only processes the zarr images in the zarr_urls, not all the\nimages in the plate. It copies all the  plate & well structure, but none\nof the image metadata or the actual image data:\n\n- For each plate, create a new OME-Zarr HCS plate with the attributes for\n    all the images in zarr_urls\n- For each well (in each plate), create a new zarr subgroup with the\n   same attributes as the original one.\n\nNote: this task makes use of methods from the `Attributes` class, see\nhttps://zarr.readthedocs.io/en/stable/api/attrs.html.\n## maximum_intensity_projection\nPerform maximum-intensity projection along Z axis.\n\nNote: this task stores the output in a new zarr file.\n",
+      "docs_info": "## copy_ome_zarr_hcs_plate\nDuplicate the OME-Zarr HCS structure for a set of zarr_urls.\n\nThis task only processes the zarr images in the zarr_urls, not all the\nimages in the plate. It copies all the  plate & well structure, but none\nof the image metadata or the actual image data:\n\n- For each plate, create a new OME-Zarr HCS plate with the attributes for\n    all the images in zarr_urls\n- For each well (in each plate), create a new zarr subgroup with the\n   same attributes as the original one.\n\nNote: this task makes use of methods from the `Attributes` class, see\nhttps://zarr.readthedocs.io/en/stable/api/attrs.html.\n## projection\nPerform intensity projection along Z axis with a chosen method.\n\nNote: this task stores the output in a new zarr file.\n",
       "docs_link": "https://fractal-analytics-platform.github.io/fractal-tasks-core"
     },
     {

fractal_tasks_core/dev/task_list.py

@@ -31,10 +31,10 @@
         meta={"cpus_per_task": 1, "mem": 4000},
     ),
     CompoundTask(
-        name="Maximum Intensity Projection HCS Plate",
+        name="Project Image (HCS Plate)",
         input_types={"is_3D": True},
         executable_init="tasks/copy_ome_zarr_hcs_plate.py",
-        executable="tasks/maximum_intensity_projection.py",
+        executable="tasks/projection.py",
         output_types={"is_3D": False},
         meta_init={"cpus_per_task": 1, "mem": 4000},
         meta={"cpus_per_task": 1, "mem": 4000},
@@ -46,13 +46,6 @@
         output_types=dict(illumination_corrected=True),
         meta={"cpus_per_task": 1, "mem": 4000},
     ),
-    # CompoundTask(
-    #     name="Illumination Correction (channel parallelized)",
-    #     input_types=dict(illumination_correction=False),
-    #     executable_init="illumination_correction_init.py",
-    #     executable="illumination_correction_compute.py",
-    #     output_types=dict(illumination_correction=True),
-    # ),
     ParallelTask(
         name="Cellpose Segmentation",
         executable="tasks/cellpose_segmentation.py",