def test_load_images(self):
"Load document's images"
source = TESTDATA / 'shapes.inselect'
with temp_directory_with_files(TESTDATA / 'shapes.inselect') as tempdir:
doc_temp = tempdir / 'shapes.inselect'
with doc_temp.open('w') as outfile, source.open() as infile:
outfile.write(infile.read())
# Document load with neither scanned image file nor thumbnail
self.assertRaises(InselectError, InselectDocument.load, doc_temp)
# Document load with thumbnail but no scanned image file
thumbnail_temp = tempdir / 'shapes_thumbnail.jpg'
thumbnail_temp.touch() # File only needs to exist
doc = InselectDocument.load(doc_temp)
self.assertFalse(doc.scanned.available)
self.assertTrue(doc.thumbnail.available)
# Document load with both scanned and thumbnail files
scanned_temp = tempdir / 'shapes.png'
scanned_temp.touch() # File only needs to exist
actual = InselectDocument.load(doc_temp)
self.assertEqual(InselectDocument.load(source).items, actual.items)
self.assertTrue(actual.scanned.available)
self.assertTrue(actual.thumbnail.available)
# Document load with scanned image file but not thumbnail
os.unlink(str(thumbnail_temp))
actual = InselectDocument.load(doc_temp)
self.assertEqual(InselectDocument.load(source).items, actual.items)
self.assertTrue(actual.scanned.available)
self.assertFalse(actual.thumbnail.available)
def test_load_images(self):
"Load document's images"
source = TESTDATA / 'shapes.inselect'
with temp_directory_with_files(TESTDATA /
'shapes.inselect') as tempdir:
doc_temp = tempdir / 'shapes.inselect'
with doc_temp.open('w') as outfile, source.open() as infile:
outfile.write(infile.read())
# Document load with neither scanned image file nor thumbnail
self.assertRaises(InselectError, InselectDocument.load, doc_temp)
# Document load with thumbnail but no scanned image file
thumbnail_temp = tempdir / 'shapes_thumbnail.jpg'
thumbnail_temp.touch() # File only needs to exist
doc = InselectDocument.load(doc_temp)
self.assertFalse(doc.scanned.available)
self.assertTrue(doc.thumbnail.available)
# Document load with both scanned and thumbnail files
scanned_temp = tempdir / 'shapes.png'
scanned_temp.touch() # File only needs to exist
actual = InselectDocument.load(doc_temp)
self.assertEqual(InselectDocument.load(source).items, actual.items)
self.assertTrue(actual.scanned.available)
self.assertTrue(actual.thumbnail.available)
# Document load with scanned image file but not thumbnail
os.unlink(str(thumbnail_temp))
actual = InselectDocument.load(doc_temp)
self.assertEqual(InselectDocument.load(source).items, actual.items)
self.assertTrue(actual.scanned.available)
self.assertFalse(actual.thumbnail.available)
def test_path_is_thumbnail_file(self):
with temp_directory_with_files() as tempdir:
thumbnail = tempdir / 'xx_thumbnail.jpg'
thumbnail.open('w') # File only needs to exist
# Thumbnail file exists but there is no corresponding .inselect doc
self.assertFalse(InselectDocument.path_is_thumbnail_file(thumbnail))
doc = tempdir / 'xx.inselect'
doc.open('w') # File only needs to exist
# Thumbnail file and corresponding .inselect file both exist
self.assertTrue(InselectDocument.path_is_thumbnail_file(thumbnail))
def test_path_is_thumbnail_file(self):
with temp_directory_with_files() as tempdir:
thumbnail = tempdir / 'xx_thumbnail.jpg'
thumbnail.touch() # File only needs to exist
# Thumbnail file exists but there is no corresponding .inselect doc
self.assertFalse(
InselectDocument.path_is_thumbnail_file(thumbnail))
doc = tempdir / 'xx.inselect'
doc.touch() # File only needs to exist
# Thumbnail file and corresponding .inselect file both exist
self.assertTrue(InselectDocument.path_is_thumbnail_file(thumbnail))
def test_save(self):
"Document save writes items"
source = TESTDATA / 'test_segment.inselect'
temp = tempfile.mkdtemp()
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA / 'test_segment.png') as tempdir:
items = [ {'fields': {}, 'rect': Rect(0.1, 0.2, 0.5, 0.5) }, ]
doc_temp = tempdir / 'test_segment.inselect'
d = InselectDocument.load(doc_temp)
d.set_items(items)
d.save()
self.assertEqual(items, InselectDocument.load(doc_temp).items)
def save_crops(dir, overwrite_existing, template):
dir = Path(dir)
export = DocumentExport(UserTemplate.load(template) if template else DWC)
for p in dir.glob('*' + InselectDocument.EXTENSION):
try:
debug_print('Loading [{0}]'.format(p))
doc = InselectDocument.load(p)
validation = export.validation_problems(doc)
if validation.any_problems:
print(
'Not saving crops for [{0}] because there are validation '
'problems'.format(p)
)
for msg in format_validation_problems(validation):
print(msg)
elif not overwrite_existing and doc.crops_dir.is_dir():
print('Crops dir [{0}] exists - skipping'.format(doc.crops_dir))
else:
print('Will save crops for [{0}] to [{1}]'.format(p, doc.crops_dir))
debug_print('Loading full-resolution scanned image')
doc.scanned.array
debug_print('Saving crops')
export.save_crops(doc)
except KeyboardInterrupt:
raise
except Exception:
print('Error saving crops from [{0}]'.format(p))
traceback.print_exc()
def test_load(self):
"Load a document from a file"
path = TESTDATA / 'test_segment.inselect'
doc = InselectDocument.load(path)
# Properties are as expected
self.assertEqual(doc.document_path, path)
self.assertEqual(5, len(doc.items))
self.assertEqual(5, doc.n_items)
self.assertEqual(doc.scanned.path, path.with_suffix('.png'))
self.assertTrue(doc.thumbnail is None)
self.assertEqual(TESTDATA / 'test_segment_crops', doc.crops_dir)
self.assertEqual('Lawrence Hudson', doc.properties['Created by'])
self.assertEqual("2015-03-14T09:19:47",
doc.properties['Created on'].strftime('%Y-%m-%dT%H:%M:%S'))
self.assertEqual('Lawrence Hudson', doc.properties['Saved by'])
self.assertEqual("2015-03-14T09:19:47",
doc.properties['Saved on'].strftime('%Y-%m-%dT%H:%M:%S'))
# Check read-only properties
with self.assertRaises(AttributeError):
doc.document_path = ''
with self.assertRaises(AttributeError):
doc.items = []
with self.assertRaises(AttributeError):
doc.crops_dir = ''
with self.assertRaises(AttributeError):
doc.n_items = 1
def test_segment_document_sort_by_columns(self):
"Segment the document with boxes sorted by columns"
doc = InselectDocument.load(TESTDATA / 'shapes.inselect')
items = doc.items
expected = doc.scanned.from_normalised(
[items[index]['rect'] for index in (0, 3, 2, 1, 4)])
self._segment(doc, True, expected)
def test_cancel_save_crops(self):
"User cancels save crops"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.load(tempdir / 'shapes.inselect')
# Create crops dir with some data
doc.crops_dir.mkdir()
with doc.crops_dir.joinpath('a_file').open('w') as outfile:
outfile.write('Some data\n')
class CancelExport(Exception):
pass
def progress(msg):
"A progress function that cancels the export"
raise CancelExport()
self.assertRaises(
CancelExport,
DocumentExport(self.TEMPLATE).save_crops, doc, progress=progress
)
# Nothing should have changed within tempdir
self.assertEqual(
['shapes.inselect', 'shapes.png', doc.crops_dir.name],
sorted(p.name for p in tempdir.iterdir()))
self.assertEqual(
['a_file'],
[p.name for p in doc.crops_dir.iterdir()]
)
def test_cancel_save_crops(self):
"User cancels save crops"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.load(tempdir / 'shapes.inselect')
# Create crops dir with some data
doc.crops_dir.mkdir()
with doc.crops_dir.joinpath('a_file').open('w') as outfile:
outfile.write('Some data\n')
class CancelExport(Exception):
pass
def progress(msg):
"A progress function that cancels the export"
raise CancelExport()
self.assertRaises(CancelExport,
DocumentExport(self.TEMPLATE).save_crops,
doc,
progress=progress)
# Nothing should have changed within tempdir
self.assertEqual(
['shapes.inselect', 'shapes.png', doc.crops_dir.name],
sorted(p.name for p in tempdir.iterdir()))
self.assertEqual(['a_file'],
[p.name for p in doc.crops_dir.iterdir()])
def test_ingest(self):
"PNG image is ingested and document is created"
inbox_img = self.inbox / 'x.png'
docs_img = self.docs / 'x.png'
shutil.copy(str(TESTDATA / 'shapes.png'), str(inbox_img))
# Read the image for comparison test
original_image = cv2.imread(str(inbox_img))
main([str(self.inbox), str(self.docs)])
# Document, scan and thumbnail should all exists
self.assertTrue((self.docs / 'x.inselect').is_file())
self.assertTrue(docs_img.is_file())
self.assertTrue((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(self.docs / 'x.inselect')
self.assertTrue(np.all(original_image == doc.scanned.array))
self.assertTrue(doc.thumbnail.available)
self.assertEqual(4096, doc.thumbnail.array.shape[1])
def save_crops(dir, overwrite_existing, template):
dir = Path(dir)
export = DocumentExport(UserTemplate.load(template) if template else DWC)
for p in dir.glob('*' + InselectDocument.EXTENSION):
try:
debug_print('Loading [{0}]'.format(p))
doc = InselectDocument.load(p)
validation = export.validation_problems(doc)
if validation.any_problems:
print(
u'Not saving crops for [{0}] because there are validation '
u'problems'.format(p)
)
for msg in format_validation_problems(validation):
print(msg)
elif not overwrite_existing and doc.crops_dir.is_dir():
print(u'Crops dir [{0}] exists - skipping'.format(doc.crops_dir))
else:
print(u'Will save crops for [{0}] to [{1}]'.format(p, doc.crops_dir))
debug_print(u'Loading full-resolution scanned image')
doc.scanned.array
debug_print(u'Saving crops')
export.save_crops(doc)
except Exception:
print(u'Error saving crops from [{0}]'.format(p))
traceback.print_exc()
def test_export_csv(self):
"Export metadata to CSV"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
# Create an empty CSV file
csv = tempdir / 'shapes.csv'
with csv.open('w'):
pass
main([str(tempdir), '--overwrite'])
csv = tempdir / 'shapes.csv'
self.assertTrue(csv.is_file())
# Check CSV contents
doc = InselectDocument.load(tempdir / 'shapes.inselect')
with csv.open('rb') as f:
res = unicodecsv.DictReader(f, encoding='utf-8')
for index, item, row in zip(count(), doc.items, res):
expected = item['fields']
expected.update({
'ItemNumber': str(1+index),
'Cropped_image_name': '{0:04}.jpg'.format(1+index)
})
actual = {
k: v for k, v in row.items()
if v and k not in BOUNDING_BOX_FIELD_NAMES
}
self.assertEqual(expected, actual)
def test_order_by_columns(self):
doc = InselectDocument.load(TESTDATA / 'shapes.inselect')
items = sort_document_items(doc.items, by_columns=True)
self.assertEqual(
['1', '4', '3', '2', '5'],
[item['fields']['catalogNumber'] for item in items]
)
def test_ingest(self):
"PNG image is ingested and document is created"
inbox_img = self.inbox / 'x.png'
docs_img = self.docs / 'x.png'
shutil.copy(str(TESTDATA / 'shapes.png'), str(inbox_img))
# Read the image for comparison test
original_image = cv2.imread(str(inbox_img))
main([str(self.inbox), str(self.docs)])
# Document, scan and thumbnail should all exists
self.assertTrue((self.docs / 'x.inselect').is_file())
self.assertTrue(docs_img.is_file())
self.assertTrue((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(self.docs / 'x.inselect')
self.assertTrue(np.all(original_image == doc.scanned.array))
self.assertTrue(doc.thumbnail.available)
self.assertEqual(4096, doc.thumbnail.array.shape[1])
def test_segment_document_sort_by_rows(self):
"Segment the document with boxes sorted by rows"
doc = InselectDocument.load(TESTDATA / 'shapes.inselect')
expected = doc.scanned.from_normalised(
[i['rect'] for i in doc.items]
)
self._segment(doc, False, expected)
def export_csv(dir, overwrite_existing, template):
dir = Path(dir)
export = DocumentExport(UserTemplate.load(template) if template else DWC)
for p in dir.glob('*' + InselectDocument.EXTENSION):
try:
debug_print('Loading [{0}]'.format(p))
doc = InselectDocument.load(p)
validation = export.validation_problems(doc)
csv_path = export.csv_path(doc)
if validation.any_problems:
print(
'Not exporting metadata for [{0}] because there are '
'validation problems'.format(p)
)
for msg in format_validation_problems(validation):
print(msg)
elif not overwrite_existing and csv_path.is_file():
print('CSV file [{0}] exists - skipping'.format(csv_path))
else:
print('Writing CSV for [{0}]'.format(p))
export.export_csv(doc)
except KeyboardInterrupt:
raise
except Exception:
print('Error saving CSV from [{0}]'.format(p))
traceback.print_exc()
def test_load(self):
"Load a document from a file"
path = TESTDATA / 'shapes.inselect'
doc = InselectDocument.load(path)
# Properties are as expected
self.assertEqual(doc.document_path, path)
self.assertEqual(5, len(doc.items))
self.assertEqual(5, doc.n_items)
self.assertEqual(doc.scanned.path, path.with_suffix('.png'))
self.assertFalse(doc.thumbnail.available)
self.assertEqual(TESTDATA / 'shapes_crops', doc.crops_dir)
self.assertEqual('Lawrence Hudson', doc.properties['Created by'])
self.assertEqual(
"2015-03-14T09:19:47",
doc.properties['Created on'].strftime('%Y-%m-%dT%H:%M:%S'))
self.assertEqual('Lawrence Hudson', doc.properties['Saved by'])
self.assertEqual(
"2015-03-14T09:19:47",
doc.properties['Saved on'].strftime('%Y-%m-%dT%H:%M:%S'))
# Check read-only properties
with self.assertRaises(AttributeError):
doc.document_path = ''
with self.assertRaises(AttributeError):
doc.items = []
with self.assertRaises(AttributeError):
doc.crops_dir = ''
with self.assertRaises(AttributeError):
doc.n_items = 1
def test_csv_export(self):
"CSV data are exported as expected"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.load(tempdir / 'shapes.inselect')
csv_path = DocumentExport(self.TEMPLATE).export_csv(doc)
self.assertEqual(csv_path, tempdir / 'shapes.csv')
# Check CSV contents
with csv_path.open('rb') as f:
reader = unicodecsv.reader(f, encoding='utf8')
headers = [
'Cropped_image_name', 'ItemNumber',
'NormalisedLeft', 'NormalisedTop', 'NormalisedRight',
'NormalisedBottom', 'ThumbnailLeft', 'ThumbnailTop',
'ThumbnailRight', 'ThumbnailBottom', 'OriginalLeft',
'OriginalTop', 'OriginalRight', 'OriginalBottom',
'catalogNumber', 'Department', 'scientificName',
'scientificName-value'
]
self.assertEqual(headers, next(reader))
# Check only the metadata columns and 'original' coordinates
# columns, ignoring thumbnail (which doesn't exist)
# and normalised (which are floating point) coordinates
metadata_cols = itemgetter(0, 1, 10, 11, 12, 13, 14, 15, 16, 17)
self.assertEqual(
('01_1.png', '1',
'0', '0', '189', '189',
'1', 'Entomology', 'A', '1'),
metadata_cols(next(reader))
)
self.assertEqual(
('02_2.png', '2',
'271', '0', '459', '189',
'2', 'Entomology', 'B', '2'),
metadata_cols(next(reader))
)
self.assertEqual(
('03_10.png', '3',
'194', '196', '257', '232',
'3', 'Entomology', 'インセクト', '10'),
metadata_cols(next(reader))
)
self.assertEqual(
('04_3.png', '4',
'0', '248', '189', '437',
'4', 'Entomology', 'Elsinoë', '3'),
metadata_cols(next(reader))
)
self.assertEqual(
('05_4.png', '5',
'271', '248', '459', '437',
'5', 'Entomology', 'D', '4'),
metadata_cols(next(reader))
)
self.assertIsNone(next(reader, None))
def test_remove_rows(self):
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
m.removeRows(0, 1)
self.assertEqual(4, m.rowCount())
expected = {"catalogNumber": "2", "scientificName": "B"}
self.assertEqual(expected, m.data(m.index(0, 0), MetadataRole))
def test_segment_document_sort_by_columns(self):
"Segment the document with boxes sorted by columns"
doc = InselectDocument.load(TESTDATA / 'shapes.inselect')
items = doc.items
expected = doc.scanned.from_normalised(
[items[index]['rect'] for index in (0, 3, 2, 1, 4)]
)
self._segment(doc, True, expected)
def test_display_role(self):
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
# First four characters only - remainder depend upon current template
self.assertEqual('0001', m.data(m.index(0, 0), Qt.DisplayRole)[:4])
self.assertEqual('0003', m.data(m.index(2, 0), Qt.DisplayRole)[:4])
self.assertEqual('0004', m.data(m.index(3, 0), Qt.DisplayRole)[:4])
def test_set_invalid_rotation(self):
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'test_segment.inselect'))
i = m.index(0, 0)
self.assertRaises(ValueError, m.setData, i, 'not an integer', RotationRole)
self.assertRaises(ValueError, m.setData, i, -1, RotationRole)
self.assertRaises(ValueError, m.setData, i, 2, RotationRole)
def test_display_role(self):
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'test_segment.inselect'))
# First four characters only - remainder depend upon current template
self.assertEqual('0001', m.data(m.index(0, 0), Qt.DisplayRole)[:4])
self.assertEqual('0003', m.data(m.index(2, 0), Qt.DisplayRole)[:4])
self.assertEqual('0004', m.data(m.index(3, 0), Qt.DisplayRole)[:4])
def test_remove_rows(self):
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'test_segment.inselect'))
m.removeRows(0, 1)
self.assertEqual(4, m.rowCount())
expected = {"catalogNumber": "2", "scientificName": "B"}
self.assertEqual(expected, m.data(m.index(0, 0), MetadataRole))
def test_remove_invalid_rows(self):
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'test_segment.inselect'))
self.assertEqual(5, m.rowCount())
self.assertRaises(ValueError, m.removeRows, -1, 1) # -ve row
self.assertRaises(ValueError, m.removeRows, 6, 1) # row > n existing rows
self.assertRaises(ValueError, m.removeRows, 0, -1) # -ve count
def test_set_items(self):
"Items are set as expected"
# TODO LH Check field validation
path = TESTDATA / 'test_segment.inselect'
doc = InselectDocument.load(path)
items = [{'fields': {}, 'rect': Rect(0, 0, 0.5, 0.5)}]
doc.set_items(items)
self.assertEqual(items, doc.items)
def test_new_from_thumbnail(self):
"Can't create a document from a thumbnail image"
with temp_directory_with_files(TESTDATA / 'test_segment.png') as tempdir:
doc = InselectDocument.new_from_scan(tempdir / 'test_segment.png')
doc.ensure_thumbnail(width=2048)
doc = None
self.assertRaises(InselectError, InselectDocument.new_from_scan,
tempdir / 'test_segment_thumbnail.png')
def test_set_same_rect_does_not_modify(self):
"Set box's rect with the same value as it currently has"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'test_segment.inselect'))
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), m.data(m.index(0, 0), RectRole), RectRole)
self.assertFalse(mock_modified_changed.called)
self.assertFalse(m.is_modified)
def test_set_metadata_modifies(self):
"Alter box's metadata"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'test_segment.inselect'))
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), {'catalogNumber': None}, MetadataRole)
mock_modified_changed.assert_called_once_with()
self.assertTrue(m.is_modified)
def test_set_rect_modifies(self):
"Alter box's rect"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), QRect(0, 0, 1, 1), RectRole)
mock_modified_changed.assert_called_once_with()
self.assertTrue(m.is_modified)
def test_set_rect_modifies(self):
"Alter box's rect"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'test_segment.inselect'))
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), QRect(0, 0, 1, 1), RectRole)
mock_modified_changed.assert_called_once_with()
self.assertTrue(m.is_modified)
def test_set_same_rect_does_not_modify(self):
"Set box's rect with the same value as it currently has"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), m.data(m.index(0, 0), RectRole), RectRole)
self.assertFalse(mock_modified_changed.called)
self.assertFalse(m.is_modified)
def test_remove_invalid_rows(self):
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
self.assertEqual(5, m.rowCount())
self.assertRaises(ValueError, m.removeRows, -1, 1) # -ve row
self.assertRaises(ValueError, m.removeRows, 6,
1) # row > n existing rows
self.assertRaises(ValueError, m.removeRows, 0, -1) # -ve count
def test_set_metadata_modifies(self):
"Alter box's metadata"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), {'catalogNumber': None}, MetadataRole)
mock_modified_changed.assert_called_once_with()
self.assertTrue(m.is_modified)
def test_set_items(self):
"Items are set as expected"
# TODO LH Check field validation
path = TESTDATA / 'shapes.inselect'
doc = InselectDocument.load(path)
items = [{'fields': {}, 'rect': Rect(0, 0, 0.5, 0.5)}]
doc.set_items(items)
self.assertEqual(items, doc.items)
def test_set_invalid_rotation(self):
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
i = m.index(0, 0)
self.assertRaises(ValueError, m.setData, i, 'not an integer',
RotationRole)
self.assertRaises(ValueError, m.setData, i, -1, RotationRole)
self.assertRaises(ValueError, m.setData, i, 2, RotationRole)
def test_set_rotation_modifies(self):
"Alter box's rotation"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), 90, RotationRole)
mock_modified_changed.assert_called_once_with()
self.assertTrue(m.is_modified)
def test_set_same_rotation_does_not_modify(self):
"Set box's rotation to the same value as it currently has"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
mock_modified_changed = self._new_mock_modified_changed(m)
m.setData(m.index(0, 0), 0, RotationRole)
self.assertFalse(mock_modified_changed.called)
self.assertFalse(m.is_modified)
def test_ensure_thumbnail(self):
"Thumbnail is created"
source_doc = TESTDATA / 'test_segment.inselect'
source_img = TESTDATA / 'test_segment.png'
with temp_directory_with_files(source_doc, source_img) as tempdir:
# Document load with no scanned image file
doc = InselectDocument.load(tempdir / 'test_segment.inselect')
self.assertTrue(doc.thumbnail is None)
doc.ensure_thumbnail(width=2048)
self.assertEqual(2048, doc.thumbnail.array.shape[1])
def test_ensure_thumbnail_silly_size(self):
"Can't create thumbnail with a silly size"
source_doc = TESTDATA / 'test_segment.inselect'
source_img = TESTDATA / 'test_segment.png'
with temp_directory_with_files(source_doc, source_img) as tempdir:
doc = InselectDocument.load(tempdir / 'test_segment.inselect')
self.assertRaises(InselectError, doc.ensure_thumbnail, -1)
self.assertRaises(InselectError, doc.ensure_thumbnail, 50)
self.assertRaises(InselectError, doc.ensure_thumbnail, 20000)
def test_save(self):
"Save document"
with temp_directory_with_files(TESTDATA / 'test_segment.inselect',
TESTDATA / 'test_segment.png') as tempdir:
items = [{
'fields': {'type': u'インセクト'},
'rect': Rect(0.1, 0.2, 0.5, 0.5),
}]
doc_temp = tempdir / 'test_segment.inselect'
d = InselectDocument.load(doc_temp)
d.set_items(items)
d.save()
self.assertEqual(items, InselectDocument.load(doc_temp).items)
# Saved on time should be within last 2 seconds
now = datetime.now(pytz.timezone("UTC"))
saved_on = d.properties['Saved on']
self.assertLessEqual((now - saved_on).seconds, 2)
def process_dir(self, dir):
# TODO LH Read image from crops dir, if it exists?
for p in dir.glob('*' + InselectDocument.EXTENSION):
# TODO LH Do not overwrite existing specimen numbers, or whatever
# field it is that barcodes are written to
print(p)
try:
self.read_barcodes_in_document(InselectDocument.load(p))
except Exception:
print('Error reading barcodes in [{0}]'.format(p))
traceback.print_exc()
def test_new_from_scan(self):
"New document is created and saved"
with temp_directory_with_files(TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.new_from_scan(tempdir / 'shapes.png')
self.assertTrue(doc.document_path.is_file())
self.assertEqual(tempdir / 'shapes.png', doc.scanned.path)
# Saved on time should be within last 2 seconds
now = datetime.now(pytz.timezone("UTC"))
created_on = doc.properties['Created on']
self.assertLessEqual((now - created_on).seconds, 2)
def test_new_from_scan(self):
"New document is created and saved"
with temp_directory_with_files(TESTDATA / 'test_segment.png') as tempdir:
doc = InselectDocument.new_from_scan(tempdir / 'test_segment.png')
self.assertTrue(doc.document_path.is_file())
self.assertEqual(tempdir / 'test_segment.png', doc.scanned.path)
# Saved on time should be within last 2 seconds
now = datetime.now(pytz.timezone("UTC"))
created_on = doc.properties['Created on']
self.assertLessEqual((now - created_on).seconds, 2)
def test_read_barcodes(self):
"Read barcodes"
with temp_directory_with_files(TESTDATA / 'barcodes.inselect',
TESTDATA / 'barcodes.jpg') as tempdir:
doc_path = tempdir.joinpath('barcodes.inselect')
# Doc should not have any catalog numbers
doc = InselectDocument.load(doc_path)
self.assertFalse(
any(v.get('fields', {}).get('catalogNumber') for v in doc.items)
)
main([str(tempdir), 'libdmtx'])
# Doc should not have expected catalog numbers
doc = InselectDocument.load(doc_path)
self.assertEqual(
['1681107', '1681110', '1681112'],
sorted(v['fields']['catalogNumber'] for v in doc.items)
)
def test_new_from_thumbnail(self):
"Can't create a document from a thumbnail image"
with temp_directory_with_files(TESTDATA / 'shapes.png') as tempdir:
doc = InselectDocument.new_from_scan(tempdir / 'shapes.png',
thumbnail_width_pixels=2048)
thumbnail = tempdir / 'shapes_thumbnail.jpg'
self.assertTrue(thumbnail.is_file())
self.assertTrue(doc.thumbnail.available)
self.assertEqual(2048, doc.thumbnail.array.shape[1])
self.assertRaises(InselectError, InselectDocument.new_from_scan,
thumbnail)
def test_read_barcodes(self):
"Read barcodes"
with temp_directory_with_files(TESTDATA / 'barcodes.inselect',
TESTDATA / 'barcodes.jpg') as tempdir:
doc_path = tempdir.joinpath('barcodes.inselect')
# Doc should not have any catalog numbers
doc = InselectDocument.load(doc_path)
self.assertFalse(
any(
v.get('fields', {}).get('catalogNumber')
for v in doc.items))
main([str(tempdir), 'libdmtx'])
# Doc should not have expected catalog numbers
doc = InselectDocument.load(doc_path)
self.assertEqual(['1681107', '1681110', '1681112'],
sorted(v['fields']['catalogNumber']
for v in doc.items))
def process_dir(self, dir):
# TODO LH Read image from crops dir, if it exists?
for p in Path(dir).glob('*' + InselectDocument.EXTENSION):
# TODO LH Do not overwrite existing object numbers, or whatever
# field it is that barcodes are written to
print(p)
try:
self.read_barcodes_in_document(InselectDocument.load(p))
except Exception:
print(u'Error reading barcodes in [{0}]'.format(p))
traceback.print_exc()
def test_crops(self):
"Cropped object images are as expected"
path = TESTDATA / 'shapes.inselect'
doc = InselectDocument.load(path)
self.assertEqual(5, len(doc.items))
# Check the contents of each crop
boxes = doc.scanned.from_normalised([i['rect'] for i in doc.items])
for box, crop in zip(boxes, doc.crops):
x0, y0, x1, y1 = box.coordinates
self.assertTrue(np.all(doc.scanned.array[y0:y1, x0:x1] == crop))
def test_crops(self):
"Cropped object images are as expected"
path = TESTDATA / 'test_segment.inselect'
doc = InselectDocument.load(path)
self.assertEqual(5, len(doc.items))
# Check the contents of each crop
boxes = doc.scanned.from_normalised([i['rect'] for i in doc.items])
for box, crop in izip(boxes, doc.crops):
x0, y0, x1, y1 = box.coordinates
self.assertTrue(np.all(doc.scanned.array[y0:y1, x0:x1] == crop))
def test_cookie_cutter(self):
"Ingested image with cookie cutter applied"
shutil.copy(unicode(TESTDATA / 'test_segment.png'),
unicode(self.inbox / 'x.png'))
main([
'--cookie-cutter={0}'.format(TESTDATA / '2x2.inselect_cookie_cutter'),
unicode(self.inbox), unicode(self.docs)
])
doc = InselectDocument.load(self.docs / 'x.inselect')
self.assertEqual(4, len(doc.items))
def test_new_from_thumbnail(self):
"Can't create a document from a thumbnail image"
with temp_directory_with_files(TESTDATA / 'test_segment.png') as tempdir:
doc = InselectDocument.new_from_scan(
tempdir / 'test_segment.png',
thumbnail_width_pixels=2048
)
thumbnail = tempdir / 'test_segment_thumbnail.jpg'
self.assertTrue(thumbnail.is_file())
self.assertEqual(2048, doc.thumbnail.array.shape[1])
self.assertRaises(InselectError, InselectDocument.new_from_scan,
thumbnail)
def test_cookie_cutter(self):
"Ingested image with cookie cutter applied"
shutil.copy(str(TESTDATA / 'shapes.png'), str(self.inbox / 'x.png'))
main([
'--cookie-cutter={0}'.format(TESTDATA /
'2x2.inselect_cookie_cutter'),
str(self.inbox),
str(self.docs)
])
doc = InselectDocument.load(self.docs / 'x.inselect')
self.assertEqual(4, len(doc.items))
def test_save(self):
"Save document"
with temp_directory_with_files(TESTDATA / 'shapes.inselect',
TESTDATA / 'shapes.png') as tempdir:
items = [{
'fields': {
'type': 'インセクト'
},
'rect': Rect(0.1, 0.2, 0.5, 0.5),
}]
doc_temp = tempdir / 'shapes.inselect'
d = InselectDocument.load(doc_temp)
d.set_items(items)
d.save()
self.assertEqual(items, InselectDocument.load(doc_temp).items)
# Saved on time should be within last 2 seconds
now = datetime.now(pytz.timezone("UTC"))
saved_on = d.properties['Saved on']
self.assertLessEqual((now - saved_on).seconds, 2)
def test_set_rect(self):
"Alter box's rect"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
i = m.index(0, 0)
r = QRect(0, 0, 1, 1)
m.setData(i, r, RectRole)
self.assertEqual(r, m.data(i, RectRole))
r = QRect(5, 5, 5, 5)
m.setData(i, r, RectRole)
self.assertEqual(r, m.data(i, RectRole))
def test_insert_row(self):
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'shapes.inselect'))
self.assertEqual(5, m.rowCount())
m.insertRow(5)
self.assertEqual(6, m.rowCount())
i = m.index(5, 0)
self.assertEqual({}, m.data(i, MetadataRole))
self.assertEqual(0, m.data(i, RotationRole))
self.assertEqual(QRect(0, 0, 0, 0), m.data(i, RectRole))
def test_set_rect(self):
"Alter box's rect"
m = Model()
m.from_document(InselectDocument.load(TESTDATA / 'test_segment.inselect'))
i = m.index(0, 0)
r = QRect(0, 0, 1, 1)
m.setData(i, r, RectRole)
self.assertEqual(r, m.data(i, RectRole))
r = QRect(5, 5, 5, 5)
m.setData(i, r, RectRole)
self.assertEqual(r, m.data(i, RectRole))
