def _metadata(path):
with ser.fileSER(path) as ser1:
data, metaData = ser1.getDataset(0) # have to get 1 image and its meta data
# Add extra meta data from the EMI file if it exists
if ser1._emi is not None:
metaData.update(ser1._emi)
metaData.update(ser1.head) # some header data for the ser file
# Clean the dictionary
for k, v in metaData.items():
if isinstance(v, bytes):
metaData[k] = v.decode('UTF8')
# Store the X and Y pixel size, offset and unit
try:
metaData['PhysicalSizeX'] = metaData['Calibration'][0]['CalibrationDelta']
metaData['PhysicalSizeXOrigin'] = metaData['Calibration'][0]['CalibrationOffset']
metaData['PhysicalSizeXUnit'] = 'm' # always meters
metaData['PhysicalSizeY'] = metaData['Calibration'][1]['CalibrationDelta']
metaData['PhysicalSizeYOrigin'] = metaData['Calibration'][1]['CalibrationOffset']
metaData['PhysicalSizeYUnit'] = 'm' # always meters
except:
metaData['PhysicalSizeX'] = 1
metaData['PhysicalSizeXOrigin'] = 0
metaData['PhysicalSizeXUnit'] = ''
metaData['PhysicalSizeY'] = 1
metaData['PhysicalSizeYOrigin'] = 0
metaData['PhysicalSizeYUnit'] = ''
metaData['FileName'] = path
return metaData
def get_tiles(self, tiling_scheme, dest_dtype="float32", roi=None):
shape = Shape((1, ) + tuple(self.shape.sig),
sig_dims=self.shape.sig.dims)
self.validate_tiling_scheme(tiling_scheme)
start = self._start_frame
stop = start + self._num_frames
if roi is None:
indices = np.arange(start, stop)
offset = start
else:
indices = _roi_to_indices(roi, start, stop)
offset = np.count_nonzero(roi.reshape((-1, ))[:start])
with fileSER(self._path) as f:
for num, idx in enumerate(indices):
tile_slice = Slice(origin=(num + offset, 0, 0), shape=shape)
data, metadata = f.getDataset(int(idx))
if data.dtype != np.dtype(dest_dtype):
data = data.astype(dest_dtype)
yield DataTile(
data.reshape(shape),
tile_slice=tile_slice,
scheme_idx=0,
)
def ser_to_png(source_file, dest_file):
""" Saves the SER source_file as PNG dest_file."""
emi_file = _discover_emi(source_file)
f = fileSER(source_file, emi_file)
ds = f.getDataset(0)
img = ds[0]
imsave(dest_file, img, format="png")
return f
def check_valid(self):
try:
with fileSER(self._path, emifile=self._emipath) as f1:
if f1.head['ValidNumberElements'] == 0:
raise DataSetException("no data found in file")
if f1.head['DataTypeID'] not in (0x4120, 0x4122):
raise DataSetException("unknown datatype id: %s" % f1.head['DataTypeID'])
return True
except (IOError, OSError) as e:
raise DataSetException("invalid dataset: %s" % e) from e
def get_tiles(self, tiling_scheme, dest_dtype="float32", roi=None):
sync_offset = self.meta.sync_offset
shape = Shape((1,) + tuple(self.shape.sig), sig_dims=self.shape.sig.dims)
self.validate_tiling_scheme(tiling_scheme)
start = self._start_frame
if start < self.meta.image_count:
stop = min(start + self._num_frames, self.meta.image_count)
if roi is None:
indices = np.arange(max(0, start), stop)
# in case of a negative sync_offset, 'start' can be negative
if start < 0:
offset = abs(sync_offset)
else:
offset = start - sync_offset
else:
indices = _roi_to_indices(roi, max(0, start), stop, sync_offset)
# in case of a negative sync_offset, 'start' can be negative
if start < 0:
offset = np.count_nonzero(roi.reshape((-1,))[:abs(sync_offset)])
else:
offset = np.count_nonzero(roi.reshape((-1,))[:start - sync_offset])
with fileSER(self._path) as f:
for num, idx in enumerate(indices):
origin = (num + offset,) + tuple([0] * self.shape.sig.dims)
tile_slice = Slice(origin=origin, shape=shape)
data, metadata = f.getDataset(int(idx))
if data.dtype != np.dtype(dest_dtype):
data = data.astype(dest_dtype)
data = data.reshape(shape)
self._preprocess(data, tile_slice)
yield DataTile(
data,
tile_slice=tile_slice,
scheme_idx=0,
)
def _get_handle(self):
return fileSER(self._path, emifile=self._emipath)
def _get_handle(self):
return fileSER(self._path)
def _get_slice(path, t):
with ser.fileSER(path) as ser_obj:
return ser_obj.getDataset(t)[0]
