Tabular threshold

transforms/tabular-thresholding-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.7-dev0
+current_version = 0.1.8-dev2
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

transforms/tabular-thresholding-tool/Dockerfile

@@ -1,9 +1,9 @@
-FROM polusai/bfio:2.3.6
+FROM polusai/bfio:2.4.5
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
-ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_TAB_EXT=".arrow"
 ENV POLUS_LOG="INFO"
 
 # Work directory defined in the base container
@@ -19,7 +19,6 @@ COPY . ${EXEC_DIR}/tabular-tools
 # Install the tool
 RUN pip3 install "${EXEC_DIR}/tabular-tools/${TOOL_DIR}" --no-cache-dir
 
-# Set the entrypoint
 # TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.tabular.transforms.tabular_thresholding"]
 CMD ["--help"]

transforms/tabular-thresholding-tool/README.md

@@ -1,4 +1,4 @@
-# Tabular Thresholding Plugin (v0.1.7-dev0)
+# Tabular Thresholding Plugin (v0.1.8-dev2)
 This plugin uses three [threshold methods](https://github.com/nishaq503/thresholding.git) to compute threshold values on a user-defined variable and then determines if each label (ROI) is above or below the calculated threshold value. A new feature column will be computed for selected threshold method with the values in  binary format (0, 1) \
 *0* `negative or below threshold`\
 *1* `positive or above threshold`
@@ -30,7 +30,7 @@ contents of `plugin.json` into the pop-up window and submit.
 
 ## Options
 
-This plugin takes 10 input arguments and one output argument:
+This plugin takes 9 input arguments and one output argument:
 
 | Name                    | Description                                         | I/O    | Type          |
 |-------------------------|-----------------------------------------------------|--------|---------------|
@@ -43,5 +43,4 @@ This plugin takes 10 input arguments and one output argument:
 | `--falsePositiverate`   | Area to the right of the threshold                  | Input  | float         |
 | `--numBins`             | Number of bins for histogram                        | Input  | number        |
 | `--n`                   | Number of standard deviation                        | Input  | number        |
-| `--outFormat`           | Output file format                                  | Input  | enum          |
 | `--outDir`              | Output collection                                   | Output | genericData   |

transforms/tabular-thresholding-tool/VERSION

@@ -1 +1 @@
-0.1.7-dev0
+0.1.8-dev2

transforms/tabular-thresholding-tool/ict.yaml

@@ -1,146 +1,135 @@
 author:
-- Hamdah Shafqat
-- Najib Ishaq
+  - Hamdah Shafqat
+  - Najib Ishaq
 contact: hamdahshafqat.abbasi@nih.gov
-container: polusai/tabular-thresholding-tool:0.1.7-dev0
-description: This plugin computes thresholds using three methods and apply thresholds
+container: polusai/tabular-thresholding-tool:0.1.8-dev2
+description:
+  This plugin computes thresholds using three methods and apply thresholds
   on each labelled data to produce binary outputs
 entrypoint: python3 -m polus.tabular.transforms.tabular_thresholding
 inputs:
-- description: Directory containing tabular data
-  format:
-  - inpDir
-  name: inpDir
-  required: true
-  type: path
-- description: Pattern to parse input files
-  format:
-  - filePattern
-  name: filePattern
-  required: false
-  type: string
-- description: FeatureName containing information about the position of non treated
-    wells
-  format:
-  - negControl
-  name: negControl
-  required: true
-  type: string
-- description: FeatureName containing information about the position of wells with
-    known treatment outcome
-  format:
-  - posControl
-  name: posControl
-  required: false
-  type: string
-- description: Name of the Variable for computing thresholds
-  format:
-  - varName
-  name: varName
-  required: true
-  type: string
-- description: Name of the threshold method
-  format:
-  - thresholdType
-  name: thresholdType
-  required: true
-  type: string
-- description: False positive rate threshold value
-  format:
-  - falsePositiverate
-  name: falsePositiverate
-  required: false
-  type: number
-- description: Number of Bins for otsu threshold
-  format:
-  - numBins
-  name: numBins
-  required: false
-  type: number
-- description: Number of Standard deviation
-  format:
-  - n
-  name: n
-  required: false
-  type: number
-- description: Output format
-  format:
-  - outFormat
-  name: outFormat
-  required: true
-  type: string
-name: polusai/tabular-thresholding-plugin
+  - description: Directory containing tabular data
+    format:
+      - inpDir
+    name: inpDir
+    required: true
+    type: path
+  - description: Pattern to parse input files
+    format:
+      - filePattern
+    name: filePattern
+    required: false
+    type: string
+  - description:
+      FeatureName containing information about the position of non treated
+      wells
+    format:
+      - negControl
+    name: negControl
+    required: true
+    type: string
+  - description:
+      FeatureName containing information about the position of wells with
+      known treatment outcome
+    format:
+      - posControl
+    name: posControl
+    required: false
+    type: string
+  - description: Name of the Variable for computing thresholds
+    format:
+      - varName
+    name: varName
+    required: true
+    type: string
+  - description: Name of the threshold method
+    format:
+      - thresholdType
+    name: thresholdType
+    required: true
+    type: string
+  - description: False positive rate threshold value
+    format:
+      - falsePositiverate
+    name: falsePositiverate
+    required: false
+    type: number
+  - description: Number of Bins for otsu threshold
+    format:
+      - numBins
+    name: numBins
+    required: false
+    type: number
+  - description: Number of Standard deviation
+    format:
+      - n
+    name: n
+    required: false
+    type: number
+name: polusai/tabular-thresholding-tool
 outputs:
-- description: Output collection
-  format:
-  - outDir
-  name: outDir
-  required: true
-  type: path
+  - description: Output collection
+    format:
+      - outDir
+    name: outDir
+    required: true
+    type: path
 repository: https://github.com/PolusAI/tabular-tools
 specVersion: 1.0.0
-title: tabular-thresholding-plugin
+title: tabular-thresholding-tool
 ui:
-- description: Input directory containing tabular data
-  key: inputs.inpDir
-  title: inpDir
-  type: path
-- description: Pattern to parse input files
-  key: inputs.filePattern
-  title: filePattern
-  type: text
-- description: FeatureName containing information about the position of non treated
-    wells
-  key: inputs.negControl
-  title: negControl
-  type: text
-- description: FeatureName containing information about the position of wells with
-    known treatment outcome
-  key: inputs.posControl
-  title: posControl
-  type: text
-- description: FeatureName containing information about the position of wells with
-    known treatment outcome
-  key: inputs.posControl
-  title: posControl
-  type: text
-- description: Name of the Variable for computing thresholds
-  key: inputs.varName
-  title: varName
-  type: text
-- description: Name of the threshold method
-  fields:
-  - fpr
-  - otsu
-  - nsigma
-  - all
-  key: inputs.thresholdType
-  title: thresholdType
-  type: select
-- default: 1.0
-  description: False positive rate threshold value
-  key: inputs.falsePositiverate
-  title: falsePositiverate
-  type: number
-- default: 512
-  description: Number of Bins for otsu threshold
-  key: inputs.numBins
-  title: numBins
-  type: number
-- default: 4
-  description: Number of Standard deviation
-  key: inputs.n
-  title: n
-  type: number
-- description: Output format
-  fields:
-  - .csv
-  - .feather
-  - .parquet
-  - .hdf5
-  - .arrow
-  - default
-  key: inputs.outFormat
-  title: outFormat
-  type: select
-version: 0.1.7-dev0
+  - description: Input directory containing tabular data
+    key: inputs.inpDir
+    title: inpDir
+    type: path
+  - description: Pattern to parse input files
+    key: inputs.filePattern
+    title: filePattern
+    type: text
+  - description:
+      FeatureName containing information about the position of non treated
+      wells
+    key: inputs.negControl
+    title: negControl
+    type: text
+  - description:
+      FeatureName containing information about the position of wells with
+      known treatment outcome
+    key: inputs.posControl
+    title: posControl
+    type: text
+  - description:
+      FeatureName containing information about the position of wells with
+      known treatment outcome
+    key: inputs.posControl
+    title: posControl
+    type: text
+  - description: Name of the Variable for computing thresholds
+    key: inputs.varName
+    title: varName
+    type: text
+  - description: Name of the threshold method
+    fields:
+      - fpr
+      - otsu
+      - nsigma
+      - all
+    key: inputs.thresholdType
+    title: thresholdType
+    type: select
+  - default: 1.0
+    description: False positive rate threshold value
+    key: inputs.falsePositiverate
+    title: falsePositiverate
+    type: number
+  - default: 512
+    description: Number of Bins for otsu threshold
+    key: inputs.numBins
+    title: numBins
+    type: number
+  - default: 4
+    description: Number of Standard deviation
+    key: inputs.n
+    title: n
+    type: number
+version: 0.1.8-dev2

transforms/tabular-thresholding-tool/package-release.sh

@@ -10,4 +10,4 @@ bump2version --config-file bumpversion.cfg --new-version ${version} --allow-dirt
 ./build-docker.sh
 
 # Push to dockerhub
-docker push polusai/tabular-thresholding-plugin:${version}
+docker push polusai/tabular-thresholding-tool:${version}

transforms/tabular-thresholding-tool/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "tabular-thresholding-plugin",
-  "version": "0.1.7-dev0",
+  "version": "0.1.8-dev2",
   "title": "tabular-thresholding-plugin",
   "description": "This plugin computes thresholds using three methods and apply thresholds on each labelled data to produce binary outputs",
   "author": "Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov), Najib Ishaq (najib.ishaq@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/tabular-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/tabular-thresholding-tool:0.1.7-dev0",
+  "containerId": "polusai/tabular-thresholding-tool:0.1.8-dev2",
   "baseCommand": [
     "python3",
     "-m",
@@ -84,22 +84,6 @@
       "type": "number",
       "options": null,
       "required": false
-    },
-    {
-      "name": "outFormat",
-      "description": "Output format",
-      "type": "enum",
-      "options": {
-        "values": [
-          ".csv",
-          ".feather",
-          ".parquet",
-          ".hdf5",
-          ".arrow",
-          "default"
-        ]
-      },
-      "required": true
     }
   ],
   "outputs": [
@@ -166,12 +150,6 @@
       "title": "n",
       "description": "Number of Standard deviation",
       "default": 4
-    },
-    {
-      "key": "inputs.outFormat",
-      "title": "outFormat",
-      "description": "Output format",
-      "default": ".arrow"
     }
   ]
 }