def test_detect_format(self):
self.assertTrue(
OpenSlide.detect_format(file_path('__missing_file')) is None)
self.assertTrue(
OpenSlide.detect_format(file_path('../setup.py')) is None)
self.assertEqual(
OpenSlide.detect_format(file_path('boxes.tiff')),
'generic-tiff')
def test_detect_format(self):
self.assertTrue(
OpenSlide.detect_format(file_path('__missing_file')) is None)
self.assertTrue(
OpenSlide.detect_format(file_path('../setup.py')) is None)
self.assertEqual(OpenSlide.detect_format(file_path('boxes.tiff')),
'generic-tiff')
def _get_slides(basedir, search='', relpath=''):
### Returns recalculatable=True if in this folder there is a .recalulatable file
children = []
for name in sorted(os.listdir(os.path.join(basedir, relpath))):
cur_relpath = os.path.join(relpath, name)
cur_path = os.path.join(basedir, cur_relpath)
if os.path.isdir(cur_path):
cur_dir = _get_slides(basedir, search, cur_relpath)
if cur_dir:
children.append({
"name":
cur_relpath,
"children":
cur_dir,
"is_folder":
True,
"recalculatable":
True if os.path.isfile(
os.path.join(cur_path, '.recalculate')) else False
})
elif OpenSlide.detect_format(cur_path):
children.append({
"name":
os.path.join(relpath, os.path.basename(cur_path)),
"is_folder":
False
})
return sorted(filter(lambda x: search in x['name'], children),
key=lambda x: x['name'])
def _fnfilter(filename):
filename = filename.lower()
if OpenSlide.detect_format(filename):
return True
elif imghdr.what(filename):
return True
elif ".tmap" in filename:
return True
return False
def __init__(self, basedir, relpath=''):
self.name = os.path.basename(relpath)
self.children = []
for name in sorted(os.listdir(os.path.join(basedir, relpath))):
cur_relpath = os.path.join(relpath, name)
cur_path = os.path.join(basedir, cur_relpath)
if os.path.isdir(cur_path):
cur_dir = _Directory(basedir, cur_relpath)
if cur_dir.children:
self.children.append(cur_dir)
elif OpenSlide.detect_format(cur_path):
self.children.append(_SlideFile(cur_relpath))
def __init__(self, basedir, relpath=''):
self.name = os.path.basename(relpath)
self.children = []
for name in sorted(os.listdir(os.path.join(basedir, relpath))):
cur_relpath = os.path.join(relpath, name)
cur_path = os.path.join(basedir, cur_relpath)
if os.path.isdir(cur_path):
cur_dir = _Directory(basedir, cur_relpath)
if cur_dir.children:
self.children.append(cur_dir)
elif OpenSlide.detect_format(cur_path):
self.children.append(_SlideFile(cur_relpath))
def __init__(self, basedir, results_file, relpath=''):
filename = []
if results_file != '':
with open(results_file, 'rb') as handle:
results = pickle.load(handle)
filename = [file.split('/')[-1] for file in results['slides']]
self.name = os.path.basename(relpath)
self.children = []
for name in sorted(os.listdir(os.path.join(basedir, relpath))):
cur_relpath = os.path.join(relpath, name)
cur_path = os.path.join(basedir, cur_relpath)
if os.path.isdir(cur_path):
cur_dir = _Directory(basedir, app.results, cur_relpath)
if cur_dir.children:
self.children.append(cur_dir)
elif results_file != '' and cur_relpath.split('/')[-1] not in filename:
continue
elif OpenSlide.detect_format(cur_path):
self.children.append(_SlideFile(cur_relpath))
def __init__(self, basedir, relpath=''):
self.name = os.path.basename(relpath)
self.full_name = '.' if relpath == '' else './' + relpath
self.children = []
self.children_masks = []
for name in sorted(os.listdir(os.path.join(basedir, relpath))):
cur_relpath = os.path.join(relpath, name)
cur_path = os.path.join(basedir, cur_relpath)
if os.path.isdir(cur_path):
cur_dir = _Directory(basedir, cur_relpath)
if cur_dir.children:
self.children.append(cur_dir)
elif OpenSlide.detect_format(cur_path):
if not ('dgai-mask' in os.path.basename(cur_path)) and not (
'dgai-uncertainty' in os.path.basename(cur_path)):
#liver-slide-1-slide.tiff -> liver-slide-1-mask.tiff
if get_mask_path(cur_path):
self.children.append(_SlideFile(cur_relpath, True))
else:
self.children.append(_SlideFile(cur_relpath, False))
def __init__(self, basedir, relpath='', max_depth=4):
self.name = os.path.basename(relpath)
self.children = []
if max_depth != 0:
try:
for name in sorted(os.listdir(os.path.join(basedir, relpath))):
cur_relpath = os.path.join(relpath, name)
cur_path = os.path.join(basedir, cur_relpath)
if os.path.isdir(cur_path):
cur_dir = _Directory(basedir,
cur_relpath,
max_depth=max_depth - 1)
if cur_dir.children:
self.children.append(cur_dir)
elif OpenSlide.detect_format(cur_path):
self.children.append(_SlideFile(cur_relpath))
elif imghdr.what(cur_path):
self.children.append(_SlideFile(cur_relpath))
except:
pass
def napari_get_reader(path):
"""A basic implementation of the napari_get_reader hook specification.
Parameters
----------
path : str or list of str
Path to file, or list of paths.
Returns
-------
function or None
If the path is a recognized format, return a function that accepts the
same path or list of paths, and returns a list of layer data tuples.
"""
if isinstance(path, list):
# Don't handle multiple paths
return None
if OpenSlide.detect_format(path) is None:
return None
try:
slide = OpenSlide(path)
except OpenSlideUnsupportedFormatError:
return None
description = slide.properties.get(PROPERTY_NAME_COMMENT)
# Don't try to handle OME-TIFF
# https://github.com/cgohlke/tifffile/blob/b346e3bd7de81de512a6715b01124c8f6d60a707/tifffile/tifffile.py#L5781
if description and description[-4:] == "OME>":
return None
# Don't try to handle files that aren't multiscale.
if slide.level_count == 1:
return None
slide.close()
return reader_function
def loadndpi(self):
self.init_scene()
formats = '*.ndpi*;;*.svs*;;*.tif*;;*.scn*;;*.mrxs*;;*.tiff*;;*.svslide*;;*.bif*'
self.path, _ = QFileDialog.getOpenFileName(
parent=self,
caption='Open file',
directory="/Users/callum/Desktop/",
filter=formats)
if self.path:
self.output = os.path.splitext(self.path)[0] + '_split'
if not os.path.exists(self.output): # make output directory
os.mkdir(self.output)
self.name = os.path.split(self.output)[-1]
self.nameLineEdit.setText(self.name)
self.load_ndpi.setStyleSheet("background-color: rgb(0,90,0)")
try:
self.image = OpenSlide(self.path)
except Exception as e:
self.loadndpi()
print(self.path + ' read to memory')
print(' slide format = ' +
str(OpenSlide.detect_format(self.path)))
if str(OpenSlide.detect_format(self.path)) == "aperio":
try:
print(
' Magnification = ' +
str(self.image.properties['openslide.objective-power'])
) # TODO
print(' Date = ' +
str(self.image.properties['aperio.Date']))
print(' dimensions = ' + str(self.image.dimensions))
print(' level_downsamples = ' +
str(self.image.level_downsamples))
except KeyError:
pass
if str(OpenSlide.detect_format(self.path)) == "hamamatsu":
try:
self.formatLineEdit.setText("Hamamatsu")
self.scanDateLineEdit.setText(
str(self.image.properties['tiff.DateTime'][:10]))
self.dimensionsLineEdit.setText(str(self.image.dimensions))
self.magnificationLineEdit.setText(
str(self.image.properties['hamamatsu.SourceLens']))
self.show_info(
f"""Magnification = {str(self.image.properties['hamamatsu.SourceLens'])}
Date = {str(self.image.properties['tiff.DateTime'])}\ndimensions = {str(self.image.dimensions)}
level_downsamples = {str(self.image.level_downsamples)}""")
print(' Magnification = ' +
str(self.image.properties['hamamatsu.SourceLens']))
print(' Date = ' +
str(self.image.properties['tiff.DateTime']))
print(' dimensions = ' + str(self.image.dimensions))
print(' level_downsamples = ' +
str(self.image.level_downsamples))
self.macro_image = self.image.associated_images['macro']
except KeyError:
pass
self.overview_level_width = 3000
self.activate([
self.nameLabel, self.nameLineEdit, self.formatLabel,
self.formatLineEdit, self.magnificationLabel,
self.magnificationLineEdit, self.scanDateLabel,
self.scanDateLineEdit, self.dimensionsLabel,
self.dimensionsLineEdit, self.overlayLevelLabel,
self.overlayLevelLineEdit, self.graphicsView, self.overlaySave,
self.groupBox_2, self.removesmallobjects
])
self.get_overview()
if os.path.exists(os.path.splitext(self.path)[0] + '.xlsx'):
self.excelpath = os.path.splitext(self.path)[0] + '.xlsx'
self.read_excel()
else:
self.excelpath = False
