fix: imagetype enum variants in manifests (#538)

PolusAI · Jul 23, 2024 · 46b072f · 46b072f
1 parent 31746f5
commit 46b072f
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Showing 8 changed files with 43 additions and 22 deletions.
diff --git a/visualization/precompute-slide-tool/.bumpversion.cfg b/visualization/precompute-slide-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.7.1
+current_version = 1.7.2-dev0
 commit = False
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
@@ -25,3 +25,5 @@ replace = version = "{new_version}"
 [bumpversion:file:README.md]
 
 [bumpversion:file:plugin.json]
+
+[bumpversion:file:ict.yml]
diff --git a/visualization/precompute-slide-tool/README.md b/visualization/precompute-slide-tool/README.md
@@ -1,4 +1,4 @@
-# Polus Precompute Slide Plugin (1.7.1)
+# Polus Precompute Slide Plugin (1.7.2-dev0)
 
 This WIPP plugin generates image pyramids in multiple viewing formats. Each
 output has a special filepattern variable that will be used to combine images
@@ -37,7 +37,22 @@ This plugin can take four types of input argument and one output argument:
 | Name          | Description                                           | I/O    | Type    |
 | ------------- | ----------------------------------------------------- | ------ | ------- |
 | `inpDir`      | Input image collection (Single Image Planes/Z Stacks) | Input  | Path    |
-| `pyramidType` | DeepZoom/Neuroglancer/Zarr                            | Input  | String  |
+| `pyramidType` | DeepZoom/Neuroglancer/Zarr                            | Input  | Enum    |
 | `filePattern` | Image pattern                                         | Input  | String  |
-| `imageType`   | Neuroglancer type (Intensity/Segmentation)            | Input  | String  |
+| `imageType`   | Neuroglancer type (Intensity/Segmentation)            | Input  | Enum    |
 | `outDir`      | Output image pyramid                                  | Output | Pyramid |
+
+### Pyramid Types
+
+Must be one of the following:
+
+- `DeepZoom`
+- `Neuroglancer`
+- `Zarr`
+
+### Image Types
+
+Must be one of the following:
+
+- `Intensity`
+- `Segmentation` (Neuroglancer only)
diff --git a/visualization/precompute-slide-tool/VERSION b/visualization/precompute-slide-tool/VERSION
@@ -1 +1 @@
-1.7.1
+1.7.2-dev0
diff --git a/visualization/precompute-slide-tool/ict.yaml → visualization/precompute-slide-tool/ict.yml b/visualization/precompute-slide-tool/ict.yaml → visualization/precompute-slide-tool/ict.yml
@@ -57,15 +57,15 @@ ui:
   title: 'Pyramid Type: '
   type: select
 - condition: inputs.pyramidType==Neuroglancer
-  description: Image or Segmentation?
+  description: Intensity or Segmentation?
   fields:
-  - image
-  - segmentation
+  - Intensity
+  - Segmentation
   key: inputs.imageType
   title: 'Image Type: '
   type: select
 - description: 'Pattern of images in input collection (image_r{rrr}_c{ccc}_z{zzz}.ome.tif). '
   key: inputs.filePattern
   title: 'Image Pattern: '
   type: text
-version: 1.7.1-dev0
+version: 1.7.2-dev0
diff --git a/visualization/precompute-slide-tool/plugin.json b/visualization/precompute-slide-tool/plugin.json
@@ -1,7 +1,7 @@
 {
   "name": "Precompute Slide",
-  "version": "1.7.1",
-  "containerId": "polusai/precompute-slide-tool:1.7.1",
+  "version": "1.7.2-dev0",
+  "containerId": "polusai/precompute-slide-tool:1.7.2-dev0",
   "baseCommand": [
     "python3",
     "-m",
@@ -36,12 +36,12 @@
     },
     {
       "name": "imageType",
-      "description": "Image is either Segmentation or Image",
+      "description": "Image is either Segmentation or Intensity",
       "type": "enum",
       "options": {
         "values": [
-          "image",
-          "segmentation"
+          "Intensity",
+          "Segmentation"
         ]
       },
       "required": false
@@ -70,13 +70,15 @@
     {
       "key": "inputs.pyramidType",
       "title": "Pyramid Type: ",
-      "description": "Build a DeepZoom, Neuroglancer, or Zarr pyramid?"
+      "description": "Build a DeepZoom, Neuroglancer, or Zarr pyramid?",
+      "default": "Zarr"
     },
     {
       "key": "inputs.imageType",
       "title": "Image Type: ",
       "description": "Image or Segmentation?",
-      "condition": "inputs.pyramidType==Neuroglancer"
+      "condition": "inputs.pyramidType==Neuroglancer",
+      "default": "Intensity"
     },
     {
       "key": "inputs.filePattern",

diff --git a/visualization/precompute-slide-tool/pyproject.toml b/visualization/precompute-slide-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-visualization-precompute-slide"
-version = "1.7.1"
+version = "1.7.2-dev0"
 description = "Polus Precompute Slide Plugin."
 authors = [
     "Madhuri Vihani <Madhuri.Vihani@nih.gov>",

diff --git a/...ization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/__main__.py b/...ization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/__main__.py
@@ -58,17 +58,17 @@ def main(  # noqa: PLR0913
         resolve_path=True,
     ),
     pyramid_type: PyramidType = typer.Option(
-        ...,
+        "Zarr",
         "--pyramidType",
         "-p",
         help="type of pyramid. Must be one of ['Neuroglancer','DeepZoom', 'Zarr']",
         case_sensitive=False,
     ),
     image_type: ImageType = typer.Option(
-        ...,
+        "Intensity",
         "--imageType",
         "-t",
-        help="type of image. Must be one of ['image','segmentation']",
+        help="type of image. Must be one of ['Intensity','Segmentation']",
         case_sensitive=False,
     ),
     preview: bool = typer.Option(

diff --git a/visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/utils.py b/visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/utils.py
@@ -37,7 +37,7 @@ class ImageType(str, enum.Enum):
     "µm": 10**3,
     "nm": 1,
     "Å": 10**-1,
-    'UnitsLength.MICROMETER': 10**3,
+    "UnitsLength.MICROMETER": 10**3,
 }
 
 # Chunk Scale
@@ -222,7 +222,9 @@ def bfio_metadata_to_slide_info(
 
         resolution = [phys_x[0] * UNITS[str(phys_x[1])]]
         resolution.append(phys_y[0] * UNITS[str(phys_y[1])])
-        resolution.append(phys_z[0] * UNITS[str(phys_z[1])])  # Just used as a placeholder
+        resolution.append(
+            phys_z[0] * UNITS[str(phys_z[1])],
+        )  # Just used as a placeholder
         dtype = str(numpy.dtype(bfio_reader.dtype))
 
     num_scales = int(numpy.ceil(numpy.log2(max(sizes))))