Work on #78

inselect/tests/test_document.py

@@ -1,7 +1,7 @@
 import json
-import unittest
 import shutil
 import tempfile
+import unittest
 
 from itertools import izip
 from pathlib import Path
@@ -14,6 +14,7 @@
 from inselect.lib.document import validate_normalised
 from inselect.lib.inselect_error import InselectError
 from inselect.lib.rect import Rect
+from inselect.lib.utils import make_readonly
 
 
 TESTDATA = Path(__file__).parent / 'test_data'
@@ -101,13 +102,31 @@ def test_save_crops(self):
             self.assertTrue(np.all(i.array==InselectImage(p).array))
 
             # Subsection of image
+            # Make sure that existing file is overwritten
             p = Path(temp) / 'partial.png'
+            p.open('w')    # File just needs to exist
             i.save_crops([Rect(0.1, 0.2, 0.4, 0.3)], [p])
             expected = i.array[87:218, 45:228]
             self.assertTrue(np.all(expected==InselectImage(p).array))
         finally:
              shutil.rmtree(temp)
 
+    def test_save_crops_read_only(self):
+        # Try to save to existing read-only file
+        temp = tempfile.mkdtemp()
+        try:
+            i = InselectImage(TESTDATA / 'test_segment.png')
+
+            p = Path(temp) / 'readonly.png'
+            p.open('w')    # File just needs to exist
+            make_readonly(p)
+
+            # Entire image
+            with self.assertRaises(InselectError):
+                i.save_crops([Rect(0, 0, 1, 1)], [p])
+        finally:
+             shutil.rmtree(temp)
+
 
 class TestDocument(unittest.TestCase):
     def test_load(self):
@@ -142,21 +161,21 @@ def test_load_images(self):
         temp = tempfile.mkdtemp()
         try:
             doc_temp = Path(temp) / 'test_segment.inselect'
-            open(str(doc_temp), 'w').write(source.open().read())
+            doc_temp.open('w').write(source.open().read())
 
             # Document load with no scanned image file
             self.assertRaises(InselectError, InselectDocument.load, doc_temp)
 
             # Document load with scanned image file present
             scanned_temp = Path(temp) / 'test_segment.png'
-            open(str(scanned_temp), 'w')       # File only needs to exist
+            scanned_temp.open('w')       # File only needs to exist
             actual = InselectDocument.load(doc_temp)
             self.assertEqual(InselectDocument.load(source).items, actual.items)
             self.assertFalse(actual.thumbnail)
 
             # Document load with scanned and thumbnail files present
             thumbnail_temp = Path(temp) / 'test_segment_thumbnail.jpg'
-            open(str(thumbnail_temp), 'w')       # File only needs to exist
+            thumbnail_temp.open('w')       # File only needs to exist
             actual = InselectDocument.load(doc_temp)
             self.assertEqual(InselectDocument.load(source).items, actual.items)
             self.assertTrue(actual.thumbnail)
@@ -168,10 +187,10 @@ def test_save(self):
         temp = tempfile.mkdtemp()
         try:
             doc_temp = Path(temp) / 'test_segment.inselect'
-            open(str(doc_temp), 'w').write(source.open().read())
+            doc_temp.open('w').write(source.open().read())
 
             scanned_temp = Path(temp) / 'test_segment.png'
-            open(str(scanned_temp), 'w')       # File only needs to exist
+            scanned_temp.open('w')       # File only needs to exist
 
             items = [ {'rect': Rect(0.1, 0.2, 0.5, 0.5) }, ]
 
@@ -241,7 +260,7 @@ def test_new_from_scan(self):
         try:
             temp = Path(temp)
             img = temp / 'test.jpg'
-            open(str(img), 'w')       # File only needs to exist
+            img.open('w')       # File only needs to exist
 
             doc = InselectDocument.new_from_scan(img)
             self.assertTrue(doc.document_path.is_file())
@@ -263,10 +282,10 @@ def test_ensure_thumbnail(self):
         temp = tempfile.mkdtemp()
         try:
             doc_temp = Path(temp) / 'test_segment.inselect'
-            open(str(doc_temp), 'w').write(source_doc.open().read())
+            doc_temp.open('w').write(source_doc.open().read())
 
             scan_tmp = Path(temp) / 'test_segment.png'
-            open(str(scan_tmp), 'wb').write(source_img.open('rb').read())
+            scan_tmp.open('wb').write(source_img.open('rb').read())
 
             # Document load with no scanned image file
             doc = InselectDocument.load(doc_temp)
@@ -276,23 +295,25 @@ def test_ensure_thumbnail(self):
         finally:
              shutil.rmtree(str(temp))
 
-    def test_ensure_thumbnail_bad_width(self):
+    def test_ensure_thumbnail_failures(self):
         source_doc = TESTDATA / 'test_segment.inselect'
         source_img = TESTDATA / 'test_segment.png'
         temp = tempfile.mkdtemp()
         try:
             doc_temp = Path(temp) / 'test_segment.inselect'
-            open(str(doc_temp), 'w').write(source_doc.open().read())
+            doc_temp.open('w').write(source_doc.open().read())
 
             scan_tmp = Path(temp) / 'test_segment.png'
-            open(str(scan_tmp), 'wb').write(source_img.open('rb').read())
+            scan_tmp.open('wb').write(source_img.open('rb').read())
 
             doc = InselectDocument.load(doc_temp)
 
             self.assertRaises(InselectError, doc.ensure_thumbnail, 50)
             self.assertRaises(InselectError, doc.ensure_thumbnail, 20000)
+
+            # TODO LH Assert that failure to create thumbnail raises
         finally:
-             shutil.rmtree(str(temp))
+            shutil.rmtree(str(temp))
 
 
 if __name__=='__main__':

inselect/tests/test_workflow.py

@@ -11,9 +11,9 @@
 
 from inselect.lib.document import InselectDocument
 from inselect.lib.inselect_error import InselectError
-from inselect.workflow.ingest import ingest
-from inselect.workflow.segment import segment_pending
-from inselect.workflow.post_process import post_process
+from inselect.workflow.ingest import ingest, ingest_image
+from inselect.workflow.segment import segment
+from inselect.workflow.read_barcodes import read_barcodes
 
 
 TESTDATA = Path(__file__).parent / 'test_data'
@@ -30,25 +30,57 @@ def tearDown(self):
         finally:
             shutil.rmtree(self.docs)
 
+class TestIngest(TestWorkflow):
+    def test_ingest_fail(self):
+        # Inbox does not exist
+        self.assertRaises(InselectError, ingest, Path('I am not a directory'),
+                          Path(self.docs))
+
+    def test_ingest_create_docs(self):
+        # Document dir should be created
+        docs = Path(self.docs) / 'I do not yet exist'
+        self.assertFalse(docs.is_dir())
+
+        img = cv2.imread(str(TESTDATA / 'test_segment.png'))
+
+        inbox_img = Path(self.inbox) / 'x.tiff'
+
+        cv2.imwrite(str(inbox_img), img)
+        ingest(self.inbox, docs)
+
+        self.assertTrue(docs.is_dir())
+
     def test_ingest(self):
         # Ingest from tiff
+        inbox_img = Path(self.inbox) / 'x.tiff'
+        docs_img = Path(self.docs) / 'x.tiff'
+
         img = cv2.imread(str(TESTDATA / 'test_segment.png'))
-        cv2.imwrite(str(Path(self.inbox) / 'x.tiff'), img)
+        cv2.imwrite(str(inbox_img), img)
 
         ingest(self.inbox, self.docs)
 
         # Document, scan and thumbnail should all exists
-        doc = InselectDocument.load(Path(self.docs) / 'x.inselect')
+        self.assertTrue((Path(self.docs) / 'x.inselect').is_file())
+        self.assertTrue(docs_img.is_file())
+        self.assertTrue((Path(self.docs) / 'x_thumbnail.jpg').is_file())
+
+        # Scan should have been removed from inbox
+        self.assertFalse(inbox_img.is_file())
 
         # Scan is as expected?
+        doc = InselectDocument.load(Path(self.docs) / 'x.inselect')
         self.assertTrue(np.all(img==doc.scanned.array))
-
         self.assertTrue(doc.thumbnail.array.shape[1], 4096)
 
         # TODO LH Assert images are read-only
-        # TODO LH Assert import of inbox/x.tiff should fail because
-        #         it exists in docs
 
+        # Call ingest_image() because ingest() swallows errors
+        cv2.imwrite(str(inbox_img), img)
+        self.assertRaises(InselectError, ingest_image, inbox_img, Path(self.docs))
+
+
+class TestSegment(TestWorkflow):
     def test_segment(self):
         # Ingest from tiff
         img = cv2.imread(str(TESTDATA / 'test_segment.png'))
@@ -59,12 +91,15 @@ def test_segment(self):
         doc = InselectDocument.load(Path(self.docs) / 'x.inselect')
         self.assertEqual(0, len(doc.items))
 
-        segment_pending(self.docs)
+        segment(self.docs)
 
         doc = InselectDocument.load(Path(self.docs) / 'x.inselect')
         self.assertEqual(5, len(doc.items))
 
-    # TODO LH test post_process
+        # TODO LH assert that segment again does not touch this document
+
+
+# TODO LH test read_barcodes
 
 
 if __name__=='__main__':

inselect/workflow/ingest.py

@@ -7,22 +7,26 @@
 
 from pathlib import Path
 
+# Import numpy here to prevent PyInstaller build from breaking
+# TODO LH find a better solution
+import numpy
 
 import inselect
 import inselect.lib.utils
 
-from inselect.lib import config
 from inselect.lib.document import InselectDocument, InselectImage
 from inselect.lib.inselect_error import InselectError
 from inselect.lib.utils import debug_print, make_readonly
 
 
-def ingest_image(source, dest):
+def ingest_image(source, dest_dir):
+    dest = dest_dir / source.name
     if source!=dest and dest.is_file():
         raise InselectError('Destination image [{0}] exists'.format(dest))
     else:
         debug_print('Ingesting [{0}] to [{1}]'.format(source, dest))
-        source.rename(dest)
+        if source!=dest:
+            source.rename(dest)
 
         # Raises if the document already exists
         doc = InselectDocument.new_from_scan(dest)
@@ -50,22 +54,23 @@ def ingest(inbox, docs):
 
     for source in inbox.glob('*tiff'):
         try:
-            dest = docs / source.name
-            ingest_image(source, dest)
+            ingest_image(source, docs)
         except Exception:
-            print('Error ingesting [{0}]'.format(source))
+            print('Error reading barcodes in [{0}] [{1}]'.format(p, source))
             traceback.print_exc()
 
 def main():
     parser = argparse.ArgumentParser(description='Ingests images into inselect')
+    parser.add_argument("inbox", help='Source directory containing scanned images')
+    parser.add_argument("docs", help='Destination directory')
     parser.add_argument('--verbose', action='store_true')
-    parser.add_argument('-v', '--version', action='version', 
+    parser.add_argument('-v', '--version', action='version',
                         version='%(prog)s ' + inselect.__version__)
     args = parser.parse_args()
 
     inselect.lib.utils.DEBUG_PRINT = args.verbose
 
-    ingest(config.inbox, config.inselect)
+    ingest(args.inbox, args.docs)
 
 if __name__=='__main__':
     main()

inselect/workflow/read_barcodes.py

@@ -6,36 +6,61 @@
 from itertools import izip
 from pathlib import Path
 
+# Import numpy here to prevent PyInstaller build from breaking
+# TODO LH find a better solution
+import numpy
 
 import inselect.lib.utils
 
-from inselect.lib import config
 from inselect.lib.utils import debug_print
 from inselect.lib.document import InselectDocument
-
-
-from gouda.bin.decode_barcode import decode_barcodes
-from gouda.decode import ZbarDecoder, SoftekDecoder
-
-
-def post_process(dir):
-    dir = Path(dir)
-
-    # TODO LH Workers from metadata config?
-    workers = [ZbarDecoder(),
-               SoftekDecoder(),
-              ]
-
+from inselect.lib.inselect_error import InselectError
+
+from gouda.strategies import roi, resize
+from gouda.engines import (AccusoftEngine, DataSymbolEngine,
+                           InliteEngine, LibDMTXEngine, StecosEngine,
+                           SoftekEngine, ZbarEngine, ZxingEngine)
+
+
+def create_datamatrix_engine():
+    # Preferred Data Matrix decoders
+    if InliteEngine.available():
+        return InliteEngine(datamatrix=True)
+    elif AccusoftEngine.available():
+        return AccusoftEngine(datamatrix=True)
+    elif SoftekEngine.available():
+        return SoftekEngine(datamatrix=True)
+    elif LibDMTXEngine.available():
+        return LibDMTXEngine()
+    else:
+        raise InselectError('No engine for Data Matrix')
+
+def read_barcodes(dir):
+    # TODO LH Engines from metadata config
+    engine = create_datamatrix_engine()
     for p in dir.glob('*' + InselectDocument.EXTENSION):
-        # TODO LH Do not do this for documents that have been post-processed
-        metadata_from_barcodes(InselectDocument.load(p), workers)
+        # TODO LH Do not overwrite existing specimen numbers or whatever field
+        # it is that barcodes are written to
+        print(p)
+        try:
+            read_barcodes_in_document(InselectDocument.load(p), engines)
+        except Exception:
+            print('Error reading barcodes in [{0}]'.format(p))
+            traceback.print_exc()
+
+def decode_barcodes(crop, engines):
+    for strategy in (resize, roi):
+        barcodes = strategy(img, engines)
+        if barcodes:
+            return barcodes
+    return []
 
-def metadata_from_barcodes(doc, workers):
+def read_barcodes_in_document(doc, engines):
     items = doc.items
     for item, crop in izip(items, doc.crops):
-        barcodes = decode_barcodes(crop, workers)
+        barcodes = decode_barcodes(crop, engines)
         if barcodes:
-            barcodes = u' '.join(barcodes)
+            barcodes = u' '.join([b.data for b in barcodes])
             debug_print('Found barcodes [{0}]'.format(barcodes))
             # TODO LH This mapping from metadata config?
             item['fields']['Specimen Number'] = barcodes
@@ -44,15 +69,18 @@ def metadata_from_barcodes(doc, workers):
     doc.save()
 
 def main():
-    parser = argparse.ArgumentParser(description='Post-processes pending documents')
+    parser = argparse.ArgumentParser(description='Read barcodes in cropped specimens')
+    parser.add_argument("dir", help='Directory containing inselect documents')
     parser.add_argument('--verbose', action='store_true')
-    parser.add_argument('-v', '--version', action='version', 
+    parser.add_argument('--debug-barcodes', action='store_true')
+    parser.add_argument('-v', '--version', action='version',
                         version='%(prog)s ' + inselect.__version__)
     args = parser.parse_args()
 
     inselect.lib.utils.DEBUG_PRINT = args.verbose
+    gouda.util.DEBUG_PRINT = args.debug_barcodes
 
-    post_process(config.inselect)
+    read_barcodes(Path(args.dir))
 
 if __name__=='__main__':
     main()