Standardized names of all updated tools.

clustering/k-means-clustering-plugin/.bumpversion.cfg → clustering/k-means-clustering-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.4-dev2
+current_version = 0.3.5-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
@@ -28,4 +28,4 @@ replace = version = "{new_version}"
 
 [bumpversion:file:CHANGELOG.md]
 
-[bumpversion:file:src/polus/plugins/clustering/k_means/__init__.py]
+[bumpversion:file:src/polus/images/clustering/k_means/__init__.py]

clustering/k-means-clustering-plugin/CHANGELOG.md → clustering/k-means-clustering-tool/CHANGELOG.md

@@ -1,4 +1,4 @@
-# K-Means Clustering(0.3.4-dev2)
+# K-Means Clustering(0.3.5-dev0)
 
 1. This plugin is updated only to the new plugin standards
 2. Before plugin support only `.csv` as an input files supported  `.csv` and `.feather` file formats. Now this plugin support other vaex supported file formats both as inputs and outputs.

clustering/k-means-clustering-plugin/Dockerfile → clustering/k-means-clustering-tool/Dockerfile

@@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src
 
 RUN pip3 install ${EXEC_DIR} --no-cache-dir
 
-ENTRYPOINT ["python3", "-m", "polus.plugins.clustering.k_means"]
+ENTRYPOINT ["python3", "-m", "polus.images.clustering.k_means"]
 CMD ["--help"]

clustering/k-means-clustering-plugin/README.md → clustering/k-means-clustering-tool/README.md

@@ -1,4 +1,4 @@
-# K-Means Clustering(v0.3.4-dev2)
+# K-Means Clustering(v0.3.5-dev0)
 
 The K-Means Clustering plugin clusters the data using Scikit-learn K-Means clustering algorithm and outputs csv file. Each instance(row) in the input csv file is assigned to one of the clusters. The output csv file contains the column 'Cluster' that shows which cluster the instance belongs to.
 

clustering/k-means-clustering-tool/VERSION

@@ -0,0 +1 @@
+0.3.5-dev0

clustering/k-means-clustering-tool/build-docker.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/k-means-clustering-tool:${version}

clustering/k-means-clustering-plugin/plugin.json → clustering/k-means-clustering-tool/plugin.json

@@ -1,18 +1,18 @@
 {
   "name": "K-Means Clustering",
-  "version": "0.3.4-dev2",
+  "version": "0.3.5-dev0",
   "title": "K-Means Clustering",
   "description": "Cluster the data using K-Means.",
   "author": "Jayapriya Nagarajan (jayapriya.nagarajan@nih.gov), Kelechi Nina Mezu (nina.mezu@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/polus-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/k-means-clustering-plugin:0.3.4-dev2",
+  "containerId": "polusai/k-means-clustering-tool:0.3.5-dev0",
   "baseCommand": [
     "python3",
     "-m",
-    "polus.plugins.clustering.k_means"
+    "polus.images.clustering.k_means"
   ],
   "inputs": [
     {

clustering/k-means-clustering-plugin/pyproject.toml → clustering/k-means-clustering-tool/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
-name = "polus-plugins-clustering-k-means"
-version = "0.3.4-dev2"
+name = "polus-images-clustering-k-means"
+version = "0.3.5-dev0"
 description = ""
 authors = [
 "Jayapriya Nagarajan <jayapriya.nagarajan@nih.gov>",

clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/__init__.py → clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/__init__.py

@@ -1,3 +1,3 @@
 """K_means clustering."""
 
-__version__ = "0.3.4-dev2"
+__version__ = "0.3.5-dev0"

clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/__main__.py → clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/__main__.py

@@ -11,14 +11,14 @@
 
 import filepattern as fp
 import typer
-from polus.plugins.clustering.k_means import k_means as km
+from polus.images.clustering.k_means import k_means as km
 
 # Initialize the logger
 logging.basicConfig(
     format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
     datefmt="%d-%b-%y %H:%M:%S",
 )
-logger = logging.getLogger("polus.plugins.clustering.k_means")
+logger = logging.getLogger("polus.images.clustering.k_means")
 logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO))
 POLUS_TAB_EXT = os.environ.get("POLUS_TAB_EXT", ".arrow")
 

clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/k_means.py → clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/k_means.py

@@ -11,8 +11,7 @@
 from sklearn.cluster import KMeans
 from sklearn.metrics import calinski_harabasz_score, davies_bouldin_score
 
-
-from polus.plugins.clustering.k_means.utils import Methods
+from .utils import Methods
 
 # Initialize the logger
 logging.basicConfig(

clustering/k-means-clustering-plugin/tests/test_main.py → clustering/k-means-clustering-tool/tests/test_main.py

@@ -5,8 +5,8 @@
 import filepattern as fp
 import pytest
 import vaex
-from polus.plugins.clustering.k_means import k_means as km
-from polus.plugins.clustering.k_means.__main__ import app
+from polus.images.clustering.k_means import k_means as km
+from polus.images.clustering.k_means.__main__ import app
 from typer.testing import CliRunner
 
 from .conftest import Generatedata

transforms/images/montage-plugin/.bumpversion.cfg → clustering/outlier-removal-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.0
+current_version = 0.2.7-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
@@ -20,10 +20,10 @@ values =
 search = version = "{current_version}"
 replace = version = "{new_version}"
 
-[bumpversion:file:plugin.json]
-
 [bumpversion:file:VERSION]
 
 [bumpversion:file:README.md]
 
-[bumpversion:file:src/polus/plugins/transforms/images/montage/__init__.py]
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/images/clustering/outlier_removal/__init__.py]

clustering/outlier-removal-plugin/CHANGELOG.md → clustering/outlier-removal-tool/CHANGELOG.md

@@ -1,10 +1,13 @@
-## [0.2.6-dev] - 2024-01-12
-### Added
+# [0.2.6-dev0] - 2024-01-12
+
+## Added
+
 - Pytests to test this plugin
 - This plugin is now installable with pip.
 - Added support for arrow file format in addition to csv
 
-### Changed
+## Changed
+
 - Updated dependencies (bfio, filepattern, preadator) to latest
 - Argparse package is replaced with Typer package for command line arguments
 - Replaced docker base image with latest container image with pre-installed bfio

clustering/outlier-removal-plugin/Dockerfile → clustering/outlier-removal-tool/Dockerfile

@@ -16,5 +16,5 @@ COPY README.md ${EXEC_DIR}
 RUN pip3 install ${EXEC_DIR} --no-cache
 
 
-ENTRYPOINT ["python3", "-m", "polus.plugins.clustering.outlier_removal"]
+ENTRYPOINT ["python3", "-m", "polus.images.clustering.outlier_removal"]
 CMD ["--help"]

clustering/outlier-removal-plugin/README.md → clustering/outlier-removal-tool/README.md

@@ -1,27 +1,31 @@
-# Outlier removal
+# Outlier removal (v0.2.7-dev0)
+
 The outlier removal plugin removes the outliers from the data based on the method selected and outputs csv file. The output will have separate csv files for inliers and outliers. The input file should be in csv format.
 
 The plugin support vaex supported input csv file that need outliers to be removed. The file should be in csv format. This is a required parameter for the plugin.
 
-## Methods:
+## Methods
+
 Choose any one of the methods mentioned to remove outliers from the data.
 
 ### Isolation Forest
+
 Ensemble-based unsupervised method for outlier detection. The algorithm isolates outliers instead of normal instances. It works based on the principle that outliers are few and different and hence, the outliers can be identified easier than the normal points. The score is calculated as the path length to isolate the observation. These two methods can be selected to detect outliers>
-1. `IsolationForest`
-Detect outliers globally that deviates significantly from the rest of the datapoints
-2. `IForest`
-Detect local outliers that are distinct when compared to those of its neighbors.
+
+1. `IsolationForest` Detect outliers globally that deviates significantly from the rest of the datapoints
+2. `IForest` Detect local outliers that are distinct when compared to those of its neighbors.
 
 
 ### Global
+
 <img src="images/Global.PNG" width="500" height="500">
 
 ### Local
 
 <img src="images/Local.PNG" width="500" height="500">
 
 ## Outputs:
+
 Select the output file by passing value to `outputType`. User can select from following options `inlier`, `oulier` or `combined`. The combined file contains `anomaly` column which score each datapoint if it is inlier or outlier.
 
 ## Building

clustering/outlier-removal-tool/VERSION

@@ -0,0 +1 @@
+0.2.7-dev0

clustering/outlier-removal-tool/build-docker.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/outlier-removal-tool:${version}

clustering/outlier-removal-plugin/plugin.json → clustering/outlier-removal-tool/plugin.json

@@ -1,18 +1,18 @@
 {
   "name": "Outlier Removal",
-  "version": "0.2.6-dev",
+  "version": "0.2.7-dev0",
   "title": "Outlier Removal",
   "description": "Remove outliers from the data.",
   "author": "Jayapriya Nagarajan (github.com/Priyaaxle) and Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/polus-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/outlier-removal-plugin:0.2.6-dev",
+  "containerId": "polusai/outlier-removal-tool:0.2.7-dev0",
   "baseCommand": [
     "python3",
     "-m",
-    "polus.plugins.clustering.outlier_removal"
+    "polus.images.clustering.outlier_removal"
   ],
   "inputs": {
     "inpDir": {

clustering/outlier-removal-plugin/pyproject.toml → clustering/outlier-removal-tool/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
-name = "polus-plugins-clustering-outlier-removal"
-version = "0.2.6-dev"
+name = "polus-images-clustering-outlier-removal"
+version = "0.2.7-dev0"
 description = "Remove outliers from the data."
 authors = [
            "Jayapriya Nagarajan <jayapriya.nagarajan@axleinfo.com>",

clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__init__.py → clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/__init__.py

@@ -1,2 +1,3 @@
 """Outlier Removal Plugin."""
-__version__ = "0.2.6-dev"
+
+__version__ = "0.2.7-dev0"

clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__main__.py → clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/__main__.py

@@ -8,7 +8,7 @@
 from typing import Optional
 
 import filepattern as fp
-import polus.plugins.clustering.outlier_removal.outlier_removal as rm
+import polus.images.clustering.outlier_removal.outlier_removal as rm
 import preadator
 import typer
 
@@ -21,7 +21,7 @@
     format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
     datefmt="%d-%b-%y %H:%M:%S",
 )
-logger = logging.getLogger("polus.plugins.clustering.outlier_removal")
+logger = logging.getLogger("polus.images.clustering.outlier_removal")
 
 
 @app.command()

clustering/outlier-removal-plugin/tests/test_cli.py → clustering/outlier-removal-tool/tests/test_cli.py

@@ -1,6 +1,6 @@
 """Test Command line Tool."""
 from typer.testing import CliRunner
-from polus.plugins.clustering.outlier_removal.__main__ import app
+from polus.images.clustering.outlier_removal.__main__ import app
 import shutil
 from pathlib import Path
 

clustering/outlier-removal-plugin/tests/test_outlier_removal.py → clustering/outlier-removal-tool/tests/test_outlier_removal.py

@@ -4,7 +4,7 @@
 
 import filepattern as fp
 import numpy as np
-import polus.plugins.clustering.outlier_removal.outlier_removal as rm
+import polus.images.clustering.outlier_removal.outlier_removal as rm
 import vaex
 
 

features/feature-segmentation-eval-tool/.bumpversion.cfg

@@ -0,0 +1,27 @@
+[bumpversion]
+current_version = 0.2.6-dev0
+commit = True
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:src/polus/images/features/feature_segmentation_eval/__init__.py]

features/feature-segmentation-eval/Dockerfile → features/feature-segmentation-eval-tool/Dockerfile

@@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src
 
 RUN pip3 install ${EXEC_DIR} --no-cache-dir
 
-ENTRYPOINT ["python3", "-m", "polus.plugins.features.feature_segmentation_eval"]
+ENTRYPOINT ["python3", "-m", "polus.images.features.feature_segmentation_eval"]
 CMD ["--help"]

features/feature-segmentation-eval-tool/VERSION

@@ -0,0 +1 @@
+0.2.6-dev0

features/feature-segmentation-eval-tool/build-docker.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/feature-segmentation-eval-tool:${version}

features/feature-segmentation-eval/plugin.json → features/feature-segmentation-eval-tool/plugin.json

@@ -1,18 +1,18 @@
 {
   "name": "Feature Segmentation Eval",
-  "version": "0.2.5-dev0",
+  "version": "0.2.6-dev0",
   "title": "Feature Segmentation Eval",
   "description": "Plugin to generate evaluation metrics for feature comparison of ground truth and predicted images.",
   "author": "Vishakha Goyal (vishakha.goyal@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/labshare/polus-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/feature-segmentation-eval:0.2.5-dev0",
+  "containerId": "polusai/feature-segmentation-eval-tool:0.2.6-dev0",
   "baseCommand": [
     "python3",
     "-m",
-    "polus.plugins.features.feature_segmentation_eval"
+    "polus.images.features.feature_segmentation_eval"
   ],
   "inputs": [
     {

features/feature-segmentation-eval/pyproject.toml → features/feature-segmentation-eval-tool/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
-name = "polus-plugins-features-feature-segmentation-eval"
-version = "0.2.5-dev0"
+name = "polus-images-features-feature-segmentation-eval"
+version = "0.2.6-dev0"
 description = "Feature segmentation eval"
 authors = [
            "Vishakha Goyal <vishakha.goyal@nih.gov>",

features/feature-segmentation-eval/src/polus/plugins/features/feature_segmentation_eval/__init__.py → features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/__init__.py

@@ -1,4 +1,4 @@
 """Feature segmentation evaluation package."""
-__version__ = "0.2.5-dev0"
+__version__ = "0.2.6-dev0"
 from . import feature_evaluation
 from . import metrics

features/feature-segmentation-eval/src/polus/plugins/features/feature_segmentation_eval/__main__.py → features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/__main__.py

@@ -7,15 +7,15 @@
 from typing import Any
 
 import filepattern as fp
-import polus.plugins.features.feature_segmentation_eval.feature_evaluation as fs
+import polus.images.features.feature_segmentation_eval.feature_evaluation as fs
 import typer
 
 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.features.feature_segmentation_eval")
+logger = logging.getLogger("polus.images.features.feature_segmentation_eval")
 logger.setLevel(POLUS_LOG)
 logging.getLogger("bfio").setLevel(POLUS_LOG)
 # Set number of threads for scalability