Merge pull request #11 from cni/intent-spectroscopy

move spectroscopy to intent

classification_from_label.py

@@ -1,26 +1,72 @@
 #!/usr/bin/env python
 '''
 Infer acquisition classification by parsing the description label.
+'''
 
+import re
 
-Example DB usage:
 
-    ## Update acquisition measurement in the DB
-    labels=list(db.acquisitions.find({},['label']))
+def feature_check(label):
+    '''Check the label for a list of features.'''
 
-    labels_only = []
-    for l in labels:
-        labels_only.append(l['label'])
+    feature_list = ['2D', 'AAscout', 'Spin-Echo', 'Gradient-Echo',
+                   'EPI', 'WASSR', 'FAIR', 'FAIREST', 'PASL', 'EPISTAR',
+                   'PICORE', 'pCASL', 'MPRAGE', 'MP2RAGE', 'FLAIR',
+                   'SWI', 'QSM', 'RMS', 'DTI', 'DSI', 'DKI', 'HARDI',
+                   'NODDI', 'Water-Reference', 'Transmit-Reference',
+                   'SBRef', 'Uniform', 'Singlerep', 'QC', 'TRACE',
+                   'FA', 'MIP', 'Navigator', 'Contrast-Agent',
+                   'Phase-Contrast', 'TOF', 'VASO', 'iVASO', 'DSC',
+                   'DCE', 'Task', 'Resting-State', 'PRESS', 'STEAM',
+                   'M0', 'Phase-Reversed', 'Spiral', 'SPGR',
+                   'Quantitative', 'Multi-Shell', 'Multi-Echo', 'Multi-Flip',
+                   'Multi-Band', 'Steady-State', '3D', 'Compressed-Sensing',
+                   'Eddy-Current-Corrected', 'Fieldmap-Corrected',
+                   'Gradient-Unwarped', 'Motion-Corrected', 'Physio-Corrected',
+                   'Derived', 'In-Plane', 'Phase', 'Magnitude']
 
-    unique_labels = set(labels_only)
-    uls = list(unique_labels)
+    return _find_matches(label, feature_list)
 
-    for l in uls:
-        measurement = infer_measurement(l)
-        db.acquisitions.update_many({'label': l}, {'$set': {'measurement': measurement}})
-'''
 
-import re
+def measurement_check(label):
+    '''Check the label for a list of measurements.'''
+
+    measurement_list = ['MRA', 'CEST', 'T1rho', 'SVS', 'CSI', 'EPSI', 'BOLD',
+                        'Phoenix','B0', 'B1', 'T1', 'T2', 'T2*', 'PD', 'MT',
+                        'Perfusion','Diffusion', 'Susceptibility', 'Fingerprinting']
+
+    return _find_matches(label, measurement_list)
+
+
+def intent_check(label):
+    '''Check the label for a list of intents.'''
+
+    intent_list = [ 'Localizer', 'Shim', 'Calibration', 'Fieldmap', 'Structural',
+                    'Functional', 'Screenshot', 'Non-Image', 'Spectroscopy' ]
+
+    return _find_matches(label, intent_list)
+
+
+def _find_matches(label, list):
+    """For a given list find those entries that match a given label."""
+
+    matches = []
+
+    for l in list:
+        regex = _compile_regex(l)
+        if regex.findall(label):
+            matches.append(l)
+
+    return matches
+
+
+def _compile_regex(string):
+    """Generate the regex for label checking"""
+
+    regex = re.compile(r"(\b%s\b)|(_%s_)|(_%s)|(%s_)" % (string,string,string,string), re.IGNORECASE)
+
+    return regex
+
 
 # Anatomy, T1
 def is_anatomy_t1(label):
@@ -310,12 +356,34 @@ def infer_classification(label):
         elif is_susceptability(label):
             classification['Measurement'] = ['Susceptability']
         elif is_spectroscopy(label):
-            classification['Measurement'] = ['Spectroscopy']
+            classification['Intent'] = ['Spectroscopy']
         elif is_phase_map(label):
             classification['Custom'] = ['Phase Map']
         elif is_screenshot(label):
             classification['Intent'] = ['Screenshot']
         else:
             print label.strip('\n') + ' --->>>> unknown'
 
+
+        # Add features to classification
+        features = feature_check(label)
+        if features:
+            class_features = classification.get('Features', [])
+            [ class_features.append(x) for x in features if x not in class_features ]
+            classification['Features'] = class_features
+
+        # Add measurements to classification
+        measurements = measurement_check(label)
+        if measurements:
+            class_measurement = classification.get('Measurement', [])
+            [ class_measurement.append(x) for x in measurements if x not in class_measurement ]
+            classification['Measurement'] = class_measurement
+
+        # Add intents to classification
+        intents = intent_check(label)
+        if intents:
+            class_intent = classification.get('Intent', [])
+            [ class_intent.append(x) for x in intents if x not in class_intent ]
+            classification['Intent'] = class_intent
+
     return classification

manifest.json

@@ -9,11 +9,11 @@
   "cite": "pfile-tools: GE P-File Utilities (https://github.com/njvack/pfile-tools)",
   "license": "BSD-2-Clause",
   "flywheel": "0",
-  "version": "1.8.0",
+  "version": "2.0.0",
   "custom": {
-    "docker-image": "stanfordcni/pfile-mr-classifier:1.8.0",
+    "docker-image": "stanfordcni/pfile-mr-classifier:2.0.0",
     "gear-builder": {
-      "image": "stanfordcni/pfile-mr-classifier:1.8.0",
+      "image": "stanfordcni/pfile-mr-classifier:2.0.0",
       "category": "converter"
     },
     "flywheel": {
@@ -25,11 +25,6 @@
       "description": "Time Zone to which all timestamps should be localized. This will set the default time zone in the Gear and thus localize the timestamps to that time zone. Examples: 'UTC', 'America/Los_Angeles', 'America/New_York'. [default = 'America/Los_Angeles'].",
       "type": "string",
       "default": "America/Los_Angeles"
-    },
-    "sync": {
-      "description": "Synchronize classification definitions with the latest known updates found at scitran-apps/dicom-mr-classifier [default = true].",
-      "type": "boolean",
-      "default": true
     }
   },
   "inputs": {

pfile-mr-classifier.py

@@ -73,13 +73,13 @@ def get_pfile_classification(pfile):
     elif PSD == 'sprl_hos':
         classification['Intent'] = ['Shim']
     elif PSD == 'spep_cni':
-        classification['Measurement'] = ['ASL']
+        classification['Measurement'] = ['Perfusion']
         classification['Intent'] = ['Functional']
     elif PSD == 'sprt':
         classification['Measurement'] = ['B0']
         classification['Intent'] = ['Fieldmap']
     elif PSD.startswith('nfl') or PSD.startswith('special') or PSD.startswith('probe-mega') or PSD.startswith('imspecial') or PSD.startswith('gaba'):
-        classification['Measurement'] = ['Spectroscopy']
+        classification['Intent'] = ['Spectroscopy']
 
     else:
         log.info("Using series description for classification!")

run

@@ -38,27 +38,6 @@ echo "$TZ" > /etc/timezone && ln -snf /usr/share/zoneinfo/"$TZ" /etc/localtime
 dpkg-reconfigure -f noninteractive tzdata
 
 
-##############################################################################
-# Handle sync option
-
-SYNC=$(parse_config 'sync')
-if [[ ${SYNC} == "true" ]]; then
-  echo -e "$CONTAINER  Syncing classification code from scitran-apps/dicom-mr-classifier/sync-classification-e4..."
-  mv ${FLYWHEEL_BASE}/classification_from_label.py /tmp
-  wget --quiet -O ${FLYWHEEL_BASE}/classification_from_label.py \
-      https://raw.githubusercontent.com/scitran-apps/dicom-mr-classifier/sync-classification-e4/classification_from_label.py
-  STAT_GET=$?
-  if [[ $STAT_GET != 0 ]]; then
-    echo -e "$CONTAINER Error during sync!"
-    mv /tmp/classification_from_label.py ${FLYWHEEL_BASE}
-  else
-    chmod +x ${FLYWHEEL_BASE}/classification_from_label.py
-  fi
-else
-  echo -e "$CONTAINER  Not syncing classification code. Using built-in version..."
-fi
-
-
 ##############################################################################
 # Check I/O directories and Generate metadata