Merge branch 'dwi'

History.rst

@@ -1,6 +1,10 @@
 This history lists major release themes. See the GitHub log
 for change details.
 
+5.2.2 / 2015-04-29
+------------------
+* Detect and stage DWI images.
+
 5.2.1 / 2015-04-29
 ------------------
 * Detect and stage ROIs.

qipipe/__init__.py

@@ -1,6 +1,6 @@
 """The top-level Quantitative Imaging Pipeline module."""
 
-__version__ = '5.2.1'
+__version__ = '5.2.2'
 """
 The one-based major.minor.patch version based on the
 `Fast and Loose Versioning <https://gist.github.com/FredLoney/6d946112e0b0f2fc4b57>`_

qipipe/staging/airc_collection.py

@@ -33,10 +33,22 @@ def collection_with_name(name):
 def _create_collections():
     """Creates the pre-defined AIRC collections."""
 
-    # The AIRC T2 scan DICOM files are in special subdirectories.
+    # The following AIRC QIN scan numbers are captured:
+    # * 1: T1
+    # * 2: T2
+    # * 4: DWI
+    # These scans have DICOM files specified by the dicom glob pattern.
+    # The T1 scan has ROI files as well, specified by the roi glob
+    # and regex patterns.
+
+    # The AIRC T2 scan DICOM files.
     breast_t2_dcm_pat = '*sorted/2_tirm_tra_bilat/*'
     sarcoma_t2_dcm_pat = '*T2*/*'
 
+    # The AIRC DWI scan DICOM files.
+    breast_dwi_dcm_pat = '*sorted/*Diffusion/*'
+    sarcoma_dwi_dcm_pat = '*Diffusion/*'
+
     # The Breast T1 scan .bqf ROI files are in the session subdirectory
     # processing/<R10 directory>/slice<slice index>/, where
     # <R10 directory> can be qualified by a lesion number.
@@ -51,7 +63,8 @@ def _create_collections():
     breast_roi_pats = ROIPatterns(glob=breast_roi_glob, regex=breast_roi_regex)
     breast_t1_pats = ScanPatterns(dicom=T1_PAT, roi=breast_roi_pats)
     breast_t2_pats = ScanPatterns(dicom=breast_t2_dcm_pat)
-    breast_scan_pats = {1: breast_t1_pats, 2: breast_t2_pats}
+    breast_dwi_pats = ScanPatterns(dicom=breast_dwi_dcm_pat)
+    breast_scan_pats = {1: breast_t1_pats, 2: breast_t2_pats, 4: breast_dwi_pats}
 
     # The Sarcoma T1 scan .bqf ROI files are in the session subdirectory
     # <processing>/<R10 directory>/slice<slice index>/, and do not
@@ -67,7 +80,8 @@ def _create_collections():
                                    regex=sarcoma_roi_regex)
     sarcoma_t1_pats = ScanPatterns(dicom=T1_PAT, roi=sarcoma_roi_pats)
     sarcoma_t2_pats = ScanPatterns(dicom=sarcoma_t2_dcm_pat)
-    sarcoma_scan_pats = {1: sarcoma_t1_pats, 2: sarcoma_t2_pats}
+    sarcoma_dwi_pats = ScanPatterns(dicom=sarcoma_dwi_dcm_pat)
+    sarcoma_scan_pats = {1: sarcoma_t1_pats, 2: sarcoma_t2_pats, 4: sarcoma_dwi_pats}
 
     # The Breast images are in BreastChemo<subject>/Visit<session>/.
     breast_opts = dict(subject='BreastChemo(\d+)', session='Visit(\d+)',

test/unit/staging/test_iterator.py

@@ -15,8 +15,9 @@ class TestStagingIterator(object):
     """iter_stage unit tests."""
     def test_breast(self):
         discovered = self._test_collection('Breast')
-        # The first visit has both a T1 and a T2 scan.
-        expected_scans = {1: set([1, 2]), 2: set([1])}
+        # The first visit has a T1, T2 and DWI scan with numbers
+        # 1, 2 and 4, resp. Visit 2 has only a T1 scan.
+        expected_scans = {1: set([1, 2, 4]), 2: set([1])}
         for visit in [1, 2]:
             session = "Session0%d" % visit
             scans = {scan_input.scan for scan_input in discovered
@@ -27,17 +28,13 @@ def test_breast(self):
         for scan_input in discovered:
             # Validate the DICOM inputs.
             if scan_input.session == "Session01":
-                # Visit 1 has two files. T1 has one 2 volumes,
-                # T2 has one volume.
+                # T1 has two volumes, T2 and DWI have one volume.
                 expected_vol_cnt = 2 if scan_input.scan == 1 else 1
                 expected_dcm_cnt = 2
-            elif scan_input.scan == 1:
+            else:
                 # Visit 2 T1 has two files in one volume.
                 expected_vol_cnt = 1
                 expected_dcm_cnt = 2
-            else:
-                # Visit 2 T2 has no scan files.
-                expected_vol_cnt = expected_dcm_cnt = 0
             dicom = scan_input.iterators.dicom
             volumes = dicom.keys()
             concat = lambda x,y: x + y
@@ -55,15 +52,19 @@ def test_breast(self):
 
             # Validate the ROI inputs.
             rois = scan_input.iterators.roi
-            if scan_input.scan == 2:
+            # Only T1 has ROIs.
+            if scan_input.scan == 1:
+                if scan_input.session == "Session01":
+                    # The first visit has two lesions.
+                    expected_lesions = set([1, 2])
+                    expected_slices = set([12, 13])
+                else:
+                    # The second visit has one lesion.
+                    expected_lesions = set([1])
+                    expected_slices = set([12, 13])
+            else:
                 expected_lesions = set([])
                 expected_slices = set([])
-            elif scan_input.session == "Session01":
-                expected_lesions = set([1, 2])
-                expected_slices = set([12, 13])
-            else:
-                expected_lesions = set([1])
-                expected_slices = set([12, 13])
             expected_roi_cnt = len(expected_lesions) * len(expected_slices)
             assert_equal(len(rois), expected_roi_cnt,
                          "%s %s scan %d input ROI file count is"