Update: Dimension Stacking Tool

formats/image-dimension-stacking-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.2
+current_version = 0.2.0-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

formats/image-dimension-stacking-tool/README.md

@@ -1,19 +1,17 @@
-# Image dimension stacking(0.1.2)
+# Image dimension stacking(0.2.0-dev0)
 
 This plugin leverages the [filepattern](https://filepattern2.readthedocs.io/en/latest/Home.html) library and employs the filepattern `groupBy` functionality to enable the matching of image filenames, facilitating their stacking into multi-dimensional images.
 
 The filepattern must include the variables `c`, `t`, and `z`. If all these variables are present in the pattern, the plugin will group images according to the order `z, c, t`. If only one variable is present in the file pattern, the plugin will group images according to that variable.
 
-
 Currently, the plugin supports the following dimensions and user can choose the relevant variable for the `groupBy` input argument.
-1.  `tubhiswt_z{z:d+}_c{c:d+}_t{t:d+}.ome.tif`\
-   Images are grouped based on `z` variable
-2. `tubhiswt_.*_.*_t{t:d+}.ome.tif`\
-   Images are grouped based on `t` variable
-3. `00001_01_{c:d+}.ome.tif`\
-   Images are grouped based on `c` variable
-
-#### Note:
+
+1. `tubhiswt_z{z:d+}_c{c:d+}_t{t:d+}.ome.tif`: Images are grouped based on `z` variable
+2. `tubhiswt_.*_.*_t{t:d+}.ome.tif`: Images are grouped based on `t` variable
+3. `00001_01_{c:d+}.ome.tif`: Images are grouped based on `c` variable
+
+## Note:
+
 Filename patterns may consist of any other filepattern variables, combined with other valid regular expression arguments, excluding the `groupBy` variable.
 
 For more information on WIPP, visit the
@@ -33,18 +31,20 @@ contents of `plugin.json` into the pop-up window and submit.
 
 This plugin takes three input argument and one output argument:
 
-| Name          | Description             | I/O    | Type   |
-|---------------|-------------------------|--------|--------|
-| `--inpDir`      | Input image collection  | Input  | Collection   |
-| `--filePattern` | Pattern to parse image files           | Input  | String |
-| `--outDir`      | Output image collection | Output | Collection   |
-| `--preview`        | Generate a JSON file to view outputs | Output | Boolean   |
+| Name            | Description                          | I/O    | Type       |
+| --------------- | ------------------------------------ | ------ | ---------- |
+| `--inpDir`      | Input image collection               | Input  | Collection |
+| `--filePattern` | Pattern to parse image files         | Input  | String     |
+| `--axis`        | Dimension to stack images            | Input  | String     |
+| `--outDir`      | Output image collection              | Output | Collection |
+| `--preview`     | Generate a JSON file to view outputs | Output | Boolean    |
 
-### Run the Docker Container
+## Run the Docker Container
 
 ```bash
-docker run -v /path/to/data:/data polusai/image-dimension-stacking-plugin:0.1.2-dev \
-  --inpDir "Path/To/Data" \
+docker run -v /path/to/data:/data polusai/image-dimension-stacking-plugin:0.2.0-dev0-dev \
+  --inpDir "path/to/data" \
   --filePattern "tubhiswt_C1-z{z:d+}.ome.tif" \
+   --axis "z" \
   --outDir "Path/To/Output/Dir"
 ```

formats/image-dimension-stacking-tool/VERSION

@@ -1 +1 @@
-0.1.2
+0.2.0-dev0

formats/image-dimension-stacking-tool/ict.yaml

@@ -1,8 +1,9 @@
 author:
 - Nick Schaub
 - Hamdah Shafqat Abbasi
+- Najib Ishaq
 contact: nick.schaub@nih.gov
-container: polusai/image-dimension-stacking-tool:0.1.2
+container: polusai/image-dimension-stacking-tool:0.2.0-dev0
 description: Stacking of image dimensions (c, z, t) to create a multidimensional image.
 entrypoint: python3 -m polus.images.formats.image_dimension_stacking
 inputs:
@@ -18,6 +19,12 @@ inputs:
   name: filePattern
   required: true
   type: string
+- description: The axis to stack the images on. One of 'c', 'z', or 't'.
+  format:
+  - string
+  name: axis
+  required: true
+  type: string
 - description: Generate an output preview
   format:
   - boolean
@@ -44,8 +51,12 @@ ui:
   key: inputs.filePattern
   title: Filename pattern
   type: text
+- description: The axis to stack the images on. One of 'c', 'z', or 't'.
+  key: inputs.axis
+  title: Axis
+  type: text
 - description: Generate an output preview
   key: inputs.preview
   title: Generate preview
   type: boolean
-version: 0.1.2-dev0
+version: 0.2.0-dev0-dev0

formats/image-dimension-stacking-tool/plugin.json

@@ -1,13 +1,13 @@
 {
   "name": "Image Dimension Stacking",
-  "version": "0.1.2",
+  "version": "0.2.0-dev0",
   "title": "Stacking of image dimensions (c, z, t) to create a multidimensional image.",
   "description": "Stacking of image dimensions (c, z, t) to create a multidimensional image.",
   "author": "Nick Schaub (nick.schaub@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
-  "containerId": "polusai/image-dimension-stacking-tool:0.1.2",
+  "containerId": "polusai/image-dimension-stacking-tool:0.2.0-dev0",
   "baseCommand": [
     "python3",
     "-m",
@@ -26,6 +26,13 @@
       "description": "Filename pattern used to separate data.",
       "required": "True"
     },
+    "axis": {
+      "type": "string",
+      "title": "Axis",
+      "description": "Axis to stack. One of 'c', 'z', 't'.",
+      "required": "False",
+      "default": "z"
+    },
     "preview": {
       "type": "boolean",
       "title": "Preview",
@@ -52,6 +59,13 @@
       "description": "Filename pattern used to separate data.",
       "required": "True"
     },
+    "axis": {
+      "type": "string",
+      "title": "Axis",
+      "description": "Axis to stack. One of 'c', 'z', 't'.",
+      "required": "False",
+      "default": "z"
+    },
     "preview": {
       "type": "boolean",
       "title": "Preview example output of this plugin",

formats/image-dimension-stacking-tool/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-formats-image-dimension-stacking"
-version = "0.1.2"
+version = "0.2.0-dev0"
 description = "Stacking multi-dimensional images"
 authors = [
            "Nick Schaub <nick.schaub@nih.gov>",
@@ -12,24 +12,20 @@ packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-bfio = {version = "2.4.1", extras = ["all"]}
+bfio = {version = "2.4.3", extras = ["all"]}
 typer = "^0.7.0"
 tqdm = "^4.66.1"
 filepattern = "^2.0.4"
-pydantic = "^1.10.4"
-preadator="0.4.0.dev2"
-numpy = "<2.0.0"
+numpy = ">=2.0,<2.1"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"
-flake8 = "^6.0.0"
 pre-commit = "^3.2.1"
-flake8-docstrings = "^1.7.0"
-black = "^23.3.0"
-mypy = "^1.1.1"
-pytest = "^7.2.2"
-ruff = "^0.0.270"
-scikit-image = "^0.22.0"
+pytest = "^8.3.2"
+pytest-sugar = "^1.0.0"
+pytest-xdist = "^3.6.1"
+scikit-image = "^0.24.0"
+scipy = "<1.14"
 
 [build-system]
 requires = ["poetry-core"]

formats/image-dimension-stacking-tool/run-plugin.sh

@@ -5,8 +5,9 @@ datapath=$(readlink --canonicalize ../data)
 
 # Inputs
 inpDir=/data/path_to_files
-
 filePattern="tubhiswt_z{z:d+}_c{c:d+}_t{t:d+}.ome.tif"
+axis="Z"
+
 # Output paths
 outDir=/data/path_to_output
 
@@ -19,4 +20,5 @@ docker run --mount type=bind,source=${datapath},target=/data/ \
             polusai/image-dimension-stacking-plugin:${version} \
             --inpDir ${inpDir} \
             --filePattern ${filePattern} \
+            --axis ${axis} \
             --outDir ${outDir}

formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/__init__.py

@@ -1,3 +1,14 @@
 """Image dimension stacking package."""
 
-__version__ = "0.1.2"
+from . import utils
+from .dimension_stacking import copy_stack
+from .dimension_stacking import write_stack
+
+__version__ = "0.2.0-dev0"
+
+__all__ = [
+    "utils",
+    "copy_stack",
+    "write_stack",
+    "__version__",
+]

formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/__main__.py

@@ -1,110 +1,105 @@
 """Image dimension stacking package."""
+
 import json
 import logging
+import os
+import pathlib
 import warnings
-from os import environ
-from pathlib import Path
-from typing import Any
 
-import filepattern as fp
-import polus.images.formats.image_dimension_stacking.dimension_stacking as st
+import filepattern
+import tqdm
 import typer
+from polus.images.formats.image_dimension_stacking import copy_stack
+from polus.images.formats.image_dimension_stacking import utils
+from polus.images.formats.image_dimension_stacking import write_stack
 
 warnings.filterwarnings("ignore")
 
 logging.basicConfig(
     format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
     datefmt="%d-%b-%y %H:%M:%S",
 )
-POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO"))
-logger = logging.getLogger("polus.plugins.formats.image_dimension_stacking")
+POLUS_LOG = getattr(logging, os.environ.get("POLUS_LOG", "INFO"))
+logger = logging.getLogger("polus.images.formats.image_dimension_stacking")
 logger.setLevel(POLUS_LOG)
-logging.getLogger("bfio").setLevel(POLUS_LOG)
-
-
-app = typer.Typer(help="Stack multi dimensional image into single image.")
-
 
-def generate_preview(out_dir: Path, file_pattern: str) -> None:
-    """Generate preview of the plugin outputs."""
-    with Path.open(Path(out_dir, "preview.json"), "w") as jfile:
-        out_json: dict[str, Any] = {
-            "filepattern": file_pattern,
-            "outDir": [],
-        }
-
-        fps = fp.FilePattern(out_dir, file_pattern)
-        out_name = fps.output_name()
-        out_json["outDir"].append(out_name)
-        json.dump(out_json, jfile, indent=2)
+app = typer.Typer()
 
 
 @app.command()
 def main(
-    inp_dir: Path = typer.Option(
+    inp_dir: pathlib.Path = typer.Option(
         ...,
         "--inpDir",
-        "-i",
         help="Path to input directory containing binary images.",
+        exists=True,
+        readable=True,
+        resolve_path=True,
+        file_okay=False,
+        dir_okay=True,
     ),
     file_pattern: str = typer.Option(
-        ".*",
+        ...,
         "--filePattern",
-        "-f",
         help="Filename pattern used to separate data.",
     ),
-    out_dir: Path = typer.Option(
+    axis: utils.StackableAxis = typer.Option(
+        utils.StackableAxis.Z,
+        "--axis",
+        help="Axis to stack images along.",
+    ),
+    out_dir: pathlib.Path = typer.Option(
         ...,
         "--outDir",
-        "-o",
         help="Output collection.",
+        exists=True,
+        writable=True,
+        resolve_path=True,
+        file_okay=False,
+        dir_okay=True,
     ),
     preview: bool = typer.Option(
         False,
         "--preview",
-        "-p",
         help="Generate preview of expected outputs.",
     ),
 ) -> None:
-    """Image dimension stacking plugin."""
-    logger.info(f"--inpDir: {inp_dir}")
-    logger.info(f"--filePattern: {file_pattern}")
-    logger.info(f"--outDir: {out_dir}")
-
-    if not inp_dir.exists():
-        msg = "inpDir does not exist"
-        raise ValueError(msg, inp_dir)
-
-    if not out_dir.exists():
-        msg = "outDir does not exist"
-        raise ValueError(msg, out_dir)
-
-    fps = fp.FilePattern(inp_dir, file_pattern)
-    list_val = ["c", "t", "z"]
-    variables = sorted([f for f in fps.get_variables() if f in list_val])
-
-    if len(variables) == 0:
-        msg = "Could not detect c, t or z variables in a pattern"
+    """Image dimension stacking tool."""
+    # Get the file pattern
+    fp = filepattern.FilePattern(inp_dir, file_pattern)
+    variables = fp.get_variables()
+
+    # Check if the axis is present among the variables
+    if axis.value not in variables:
+        msg = f"Axis {axis} not present among the variables {variables}."
+        logger.error(msg)
         raise ValueError(msg)
 
-    if variables == list_val or variables == ["z"]:
-        group_by = "z"
-
-    if variables == ["c", "t"] or variables == ["c"]:
-        group_by = "c"
+    # Collect the files into groups to stack
+    groups: dict[pathlib.Path, list[pathlib.Path]] = {}
 
-    if variables == ["t"]:
-        group_by = "t"
+    # Group the files by all variables except the axis
+    group_by = [v for v in variables if v != axis.value]
+    for _, files in fp(group_by=group_by):
+        out_path = out_dir / fp.output_name(files)
+        groups[out_path] = [p for _, [p] in files]
 
     if preview:
-        generate_preview(out_dir=out_dir, file_pattern=file_pattern)
-
-    st.dimension_stacking(
-        inp_dir=inp_dir,
-        file_pattern=file_pattern,
-        group_by=group_by,
-        out_dir=out_dir,
-    )
+        with (out_dir / "preview.json").open("w") as f:
+            preview_data = {"outDir": [str(p) for p in groups]}
+            json.dump(preview_data, f, indent=2)
+        return
+
+    # TODO: Use some parallelism here
+    for out_path, inp_paths in tqdm.tqdm(
+        groups.items(),
+        desc="Stacking groups",
+        total=len(groups),
+    ):
+        if str(out_path).endswith(".ome.zarr"):
+            copy_stack(inp_paths, axis, out_path)
+        else:
+            write_stack(inp_paths, axis, out_path)
 
 
 if __name__ == "__main__":