adding reference_feature code and dependencies

Dockerfile

@@ -134,6 +134,6 @@ WORKDIR $mc_path/multic/cli
 RUN python -m slicer_cli_web.cli_list_entrypoint --list_cli
 RUN python -m slicer_cli_web.cli_list_entrypoint MultiCompartmentSegment --help
 RUN python -m slicer_cli_web.cli_list_entrypoint FeatureExtraction --help
-
+RUN python -m slicer_cli_web.cli_list_entrypoint ReferenceFeatureExtraction --help
 
 ENTRYPOINT ["/bin/bash", "docker-entrypoint.sh"]

multic/cli/ReferenceFeatureExtraction/ReferenceFeatureExtraction.py

@@ -0,0 +1,57 @@
+import os
+import sys
+from glob import glob
+import girder_client
+from ctk_cli import CLIArgumentParser
+
+sys.path.append("..")
+from segmentationschool.utils.json_to_xml import get_xml_path
+
+NAMES = ['cortical_interstitium','medullary_interstitium','non_globally_sclerotic_glomeruli','globally_sclerotic_glomeruli','tubules','arteries/arterioles']
+
+
+def main(args):
+
+    folder = args.base_dir
+    wsi = args.input_file
+    file_name = wsi.split('/')[-1]
+    base_dir_id = folder.split('/')[-2]
+    _ = os.system("printf '\nUsing data from girder_client Folder: {}\n'".format(folder))
+
+    gc = girder_client.GirderClient(apiUrl=args.girderApiUrl)
+    gc.setToken(args.girderToken)
+    # get files in folder
+    files = list(gc.listItem(base_dir_id))
+    # dict to link filename to gc id
+    item_dict = dict()
+    for file in files:
+        d = {file['name']:file['_id']}
+        item_dict.update(d)
+
+    file_id = item_dict[file_name]
+
+    cwd = os.getcwd()
+    print(cwd)
+    os.chdir(cwd)
+    tmp = folder
+    _ = os.system("printf '\n---\n\nFOUND: [{}]\n'".format(file_name))
+    # get annotation
+    annotations= gc.get('/annotation/item/{}'.format(file_id), parameters={'sort': 'updated'})
+    annotations.reverse()
+    annotations = list(annotations)
+
+    annotations_filtered = [annot for annot in annotations if annot['annotation']['name'].strip() in NAMES]
+    _ = os.system("printf '\tfound [{}] annotation layers...\n'".format(len(annotations_filtered)))
+    del annotations
+    # create root for xml file
+
+    xml_path = get_xml_path(annotations_filtered, NAMES, tmp, file_name)    
+    _ = os.system("printf '\ndone retriving data...\n\n'")
+
+    cmd = "python3 ../segmentationschool/segmentation_school.py --option {} --base_dir {} --file {} --xml_path {} --platform {} --item_id {} --girderApiUrl {} --girderToken {}".format('get_features', args.base_dir, args.input_file, xml_path, 'DSA',file_id, args.girderApiUrl, args.girderToken)
+    print(cmd)
+    sys.stdout.flush()
+    os.system(cmd)
+
+if __name__ == "__main__":
+    main(CLIArgumentParser().parse_args())

multic/cli/ReferenceFeatureExtraction/ReferenceFeatureExtraction.xml

@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<executable>
+  <category>HistomicsTK</category>
+  <title>Extract Extended Clinical Features</title>
+  <description>Extract reference features</description>
+  <version>0.1.0</version>
+  <documentation-url>https://github.com/SarderLab/Multi-Compartment-Segmentation</documentation-url>
+  <license>Apache 2.0</license>
+  <contributor>Sayat Mimar (UFL)</contributor>
+  <acknowledgements>This work is part of efforts in digital pathology by the Sarder Lab: UFL.</acknowledgements>
+  <parameters>
+    <label>IO</label>
+    <description>Input/output parameters</description>
+    <image>
+      <name>input_file</name>
+      <label>input_file</label>
+      <description>input file</description>
+      <channel>input</channel>
+      <index>0</index>
+    </image>
+    <directory>
+      <name>base_dir</name>
+      <label>Base Directory</label>
+      <description>Base Directory for the model</description>
+      <channel>input</channel>
+      <index>1</index>
+    </directory>
+  </parameters>
+  <parameters advanced="true">
+    <label>Girder API URL and Key</label>
+    <description>A Girder API URL and token for Girder client</description>
+    <string>
+      <name>girderApiUrl</name>
+      <longflag>api-url</longflag>
+      <label>Girder API URL</label>
+      <description>A Girder API URL (e.g., https://girder.example.com:443/api/v1)</description>
+      <default></default>
+    </string>
+    <string>
+      <name>girderToken</name>
+      <longflag>token</longflag>
+      <label>Girder API Token</label>
+      <description>A Girder token</description>
+      <default></default>
+    </string>
+  </parameters>
+</executable>

multic/cli/slicer_cli_list.json

@@ -4,5 +4,8 @@
   },
   "FeatureExtraction": {
     "type"    : "python"
+  },
+  "ReferenceFeatureExtraction": {
+    "type"    : "python"
   }
 }