Rename maximum intensity projection to projection

Author: jluethi

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/dev/task_list.py

@@ -34,7 +34,7 @@
         name="HCS Plate Intensity Projection",
         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},

fractal_tasks_core/tasks/maximum_intensity_projection.py fractal_tasks_core/tasks/projection.py

@@ -37,7 +37,7 @@
 
 
 @validate_call
-def maximum_intensity_projection(
+def projection(
     *,
     # Fractal parameters
     zarr_url: str,
@@ -46,7 +46,7 @@ def maximum_intensity_projection(
     overwrite: bool = False,
 ) -> dict[str, Any]:
     """
-    Perform maximum-intensity projection along Z axis.
+    Perform intensity projection along Z axis with a chosen method.
 
     Note: this task stores the output in a new zarr file.
 
@@ -191,6 +191,6 @@ def maximum_intensity_projection(
     from fractal_tasks_core.tasks._utils import run_fractal_task
 
     run_fractal_task(
-        task_function=maximum_intensity_projection,
+        task_function=projection,
         logger_name=logger.name,
     )

tests/tasks/test_import_ome_zarr.py

@@ -8,8 +8,8 @@
     copy_ome_zarr_hcs_plate,
 )
 from fractal_tasks_core.tasks.import_ome_zarr import import_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.channels import ChannelInputModel
@@ -71,7 +71,7 @@ def test_import_ome_zarr_plate(tmp_path, zenodo_zarr):
     debug(parallelization_list)
 
     for image in parallelization_list:
-        maximum_intensity_projection(
+        projection(
             zarr_url=image["zarr_url"],
             init_args=image["init_args"],
             overwrite=True,
@@ -258,7 +258,7 @@ def test_import_ome_zarr_plate_no_ROI_tables(tmp_path, zenodo_zarr):
     debug(parallelization_list)
 
     for image in parallelization_list:
-        maximum_intensity_projection(
+        projection(
             zarr_url=image["zarr_url"],
             init_args=image["init_args"],
             overwrite=True,

tests/tasks/test_registration.py

@@ -56,8 +56,8 @@
     init_group_by_well_for_multiplexing,
 )
 from fractal_tasks_core.tasks.io_models import MultiplexingAcquisition
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.utils import _split_well_path_image_path
 
@@ -296,7 +296,7 @@ def test_multiplexing_registration(
     # # MIP
     image_list_updates = []
     for image in parallelization_list:
-        image_list_updates += maximum_intensity_projection(
+        image_list_updates += projection(
             zarr_url=image["zarr_url"],
             init_args=image["init_args"],
             overwrite=True,

tests/tasks/test_workflows.py

@@ -34,8 +34,8 @@
 from fractal_tasks_core.tasks.illumination_correction import (
     illumination_correction,
 )
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.zarr_utils import OverwriteNotAllowedError
 
@@ -350,7 +350,7 @@ def test_MIP(
     # MIP
     image_list_updates = []
     for image in parallelization_list:
-        image_list_updates += maximum_intensity_projection(
+        image_list_updates += projection(
             zarr_url=image["zarr_url"],
             init_args=image["init_args"],
             overwrite=True,
@@ -369,7 +369,7 @@ def test_MIP(
 
     # Re-run with overwrite=True
     for image in parallelization_list:
-        maximum_intensity_projection(
+        projection(
             zarr_url=image["zarr_url"],
             init_args=image["init_args"],
             overwrite=True,
@@ -378,7 +378,7 @@ def test_MIP(
     # Re-run with overwrite=False
     with pytest.raises(OverwriteNotAllowedError):
         for image in parallelization_list:
-            maximum_intensity_projection(
+            projection(
                 zarr_url=image["zarr_url"],
                 init_args=image["init_args"],
                 overwrite=False,
@@ -458,7 +458,7 @@ def test_MIP_subset_of_images(
 
     # MIP
     for image in parallelization_list:
-        maximum_intensity_projection(
+        projection(
             zarr_url=image["zarr_url"],
             init_args=image["init_args"],
             overwrite=True,

tests/tasks/test_workflows_cellpose_segmentation.py

@@ -54,8 +54,8 @@
 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,
 )
 from fractal_tasks_core.zarr_utils import OverwriteNotAllowedError
 
@@ -484,7 +484,7 @@ def test_workflow_with_per_well_labeling_2D(
     # MIP
     image_list_updates = []
     for image in parallelization_list:
-        image_list_updates += maximum_intensity_projection(
+        image_list_updates += projection(
             zarr_url=image["zarr_url"],
             init_args=image["init_args"],
             overwrite=True,

tests/tasks/test_workflows_multiplexing.py

@@ -30,8 +30,8 @@
     copy_ome_zarr_hcs_plate,
 )
 from fractal_tasks_core.tasks.io_models import MultiplexingAcquisition
-from fractal_tasks_core.tasks.maximum_intensity_projection import (
-    maximum_intensity_projection,
+from fractal_tasks_core.tasks.projection import (
+    projection,
 )
 from fractal_tasks_core.zarr_utils import OverwriteNotAllowedError
 
@@ -407,7 +407,7 @@ def test_multiplexing_MIP(
     # MIP
     image_list_updates = []
     for image in parallelization_list:
-        image_list_updates += maximum_intensity_projection(
+        image_list_updates += projection(
             zarr_url=image["zarr_url"],
             init_args=image["init_args"],
             overwrite=True,