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Black formatting #14

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merged 2 commits into from
Dec 4, 2022
Merged

Black formatting #14

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687d50b
adopt black formatting
ziw-liu Dec 2, 2022
986de34
add .git-blame-ignore-revs file
ziw-liu Dec 2, 2022
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4 changes: 4 additions & 0 deletions .git-blame-ignore-revs
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# .git-blame-ignore-revs
# created as described in: https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view
# adopt black formatting
687d50b983202a684b8d884c508e01af85233df2
2 changes: 1 addition & 1 deletion iohub/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@
# -*- coding: utf-8 -*-

from .reader import WaveorderReader
from .writer import WaveorderWriter
from .writer import WaveorderWriter
148 changes: 84 additions & 64 deletions iohub/multipagetiff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@


class MicromanagerOmeTiffReader(ReaderBase):

def __init__(self, folder: str, extract_data: bool = False):
super().__init__()

Expand All @@ -23,16 +22,18 @@ def __init__(self, folder: str, extract_data: bool = False):
"""

# Add Initial Checks
if len(glob.glob(os.path.join(folder, '*.ome.tif'))) == 0:
raise ValueError('Specific input contains no ome.tif files, please specify a valid input directory')
if len(glob.glob(os.path.join(folder, "*.ome.tif"))) == 0:
raise ValueError(
"Specific input contains no ome.tif files, please specify a valid input directory"
)

# ignore tiffile warnings, doesn't work
with warnings.catch_warnings():
warnings.simplefilter('ignore', tiff)
warnings.simplefilter("ignore", tiff)

# Grab all image files
self.data_directory = folder
self._files = glob.glob(os.path.join(self.data_directory, '*.ome.tif'))
self._files = glob.glob(os.path.join(self.data_directory, "*.ome.tif"))

# Generate Data Specific Properties
self.coords = None
Expand Down Expand Up @@ -79,31 +80,31 @@ def _gather_index_maps(self):
slices = 0
for file in self._files:
tf = TiffFile(file)
meta = tf.micromanager_metadata['IndexMap']
meta = tf.micromanager_metadata["IndexMap"]
tf.close()
offsets = list(meta['Offset'])
offsets = list(meta["Offset"])

for page in range(len(meta['Channel'])):
for page in range(len(meta["Channel"])):
coord = [0, 0, 0, 0]
coord[0] = meta['Position'][page]
coord[1] = meta['Frame'][page]
coord[2] = meta['Channel'][page]
coord[3] = meta['Slice'][page]
coord[0] = meta["Position"][page]
coord[1] = meta["Frame"][page]
coord[2] = meta["Channel"][page]
coord[3] = meta["Slice"][page]
offset = self._get_byte_offset(offsets, page)
self.coord_map[tuple(coord)] = (file, page, offset)

# update dimensions as we go along, helps with incomplete datasets
if coord[0]+1 > positions:
positions = coord[0]+1
if coord[0] + 1 > positions:
positions = coord[0] + 1

if coord[1]+1 > frames:
frames = coord[1]+1
if coord[1] + 1 > frames:
frames = coord[1] + 1

if coord[2]+1 > channels:
channels = coord[2]+1
if coord[2] + 1 > channels:
channels = coord[2] + 1

if coord[3]+1 > slices:
slices = coord[3]+1
if coord[3] + 1 > slices:
slices = coord[3] + 1

# update dimensions to the largest dimensions present in the saved data
self.positions = positions
Expand Down Expand Up @@ -133,7 +134,6 @@ def _get_byte_offset(self, offsets, page):

return array_offset


def _set_mm_meta(self):
"""
assign image metadata from summary metadata
Expand All @@ -145,46 +145,56 @@ def _set_mm_meta(self):
with TiffFile(self._files[0]) as tif:
self.mm_meta = tif.micromanager_metadata

mm_version = self.mm_meta['Summary']['MicroManagerVersion']
if 'beta' in mm_version:
if self.mm_meta['Summary']['Positions'] > 1:
mm_version = self.mm_meta["Summary"]["MicroManagerVersion"]
if "beta" in mm_version:
if self.mm_meta["Summary"]["Positions"] > 1:
self.stage_positions = []

for p in range(len(self.mm_meta['Summary']['StagePositions'])):
pos = self._simplify_stage_position_beta(self.mm_meta['Summary']['StagePositions'][p])
for p in range(
len(self.mm_meta["Summary"]["StagePositions"])
):
pos = self._simplify_stage_position_beta(
self.mm_meta["Summary"]["StagePositions"][p]
)
self.stage_positions.append(pos)

# MM beta versions sometimes don't have 'ChNames', so I'm wrapping in a try-except and setting the
# channel names to empty strings if it fails.
try:
for ch in self.mm_meta['Summary']['ChNames']:
for ch in self.mm_meta["Summary"]["ChNames"]:
self.channel_names.append(ch)
except:
self.channel_names = self.mm_meta['Summary']['Channels']*[''] # empty strings

elif mm_version == '1.4.22':
for ch in self.mm_meta['Summary']['ChNames']:
self.channel_names = self.mm_meta["Summary"][
"Channels"
] * [
""
] # empty strings

elif mm_version == "1.4.22":
for ch in self.mm_meta["Summary"]["ChNames"]:
self.channel_names.append(ch)

else:
if self.mm_meta['Summary']['Positions'] > 1:
if self.mm_meta["Summary"]["Positions"] > 1:
self.stage_positions = []

for p in range(self.mm_meta['Summary']['Positions']):
pos = self._simplify_stage_position(self.mm_meta['Summary']['StagePositions'][p])
for p in range(self.mm_meta["Summary"]["Positions"]):
pos = self._simplify_stage_position(
self.mm_meta["Summary"]["StagePositions"][p]
)
self.stage_positions.append(pos)

for ch in self.mm_meta['Summary']['ChNames']:
for ch in self.mm_meta["Summary"]["ChNames"]:
self.channel_names.append(ch)

# dimensions based on mm metadata do not reflect final written dimensions
# these will change after data is loaded
self.z_step_size = self.mm_meta['Summary']['z-step_um']
self.height = self.mm_meta['Summary']['Height']
self.width = self.mm_meta['Summary']['Width']
self.frames = self.mm_meta['Summary']['Frames']
self.slices = self.mm_meta['Summary']['Slices']
self.channels = self.mm_meta['Summary']['Channels']
self.z_step_size = self.mm_meta["Summary"]["z-step_um"]
self.height = self.mm_meta["Summary"]["Height"]
self.width = self.mm_meta["Summary"]["Width"]
self.frames = self.mm_meta["Summary"]["Frames"]
self.slices = self.mm_meta["Summary"]["Slices"]
self.channels = self.mm_meta["Summary"]["Channels"]

def _simplify_stage_position(self, stage_pos: dict):
"""
Expand All @@ -200,9 +210,9 @@ def _simplify_stage_position(self, stage_pos: dict):
"""

out = copy(stage_pos)
out.pop('DevicePositions')
for dev_pos in stage_pos['DevicePositions']:
out.update({dev_pos['Device']: dev_pos['Position_um']})
out.pop("DevicePositions")
for dev_pos in stage_pos["DevicePositions"]:
out.update({dev_pos["Device"]: dev_pos["Position_um"]})
return out

def _simplify_stage_position_beta(self, stage_pos: dict):
Expand All @@ -221,19 +231,19 @@ def _simplify_stage_position_beta(self, stage_pos: dict):
"""

new_dict = {}
new_dict['Label'] = stage_pos['label']
new_dict['GridRow'] = stage_pos['gridRow']
new_dict['GridCol'] = stage_pos['gridCol']
new_dict["Label"] = stage_pos["label"]
new_dict["GridRow"] = stage_pos["gridRow"]
new_dict["GridCol"] = stage_pos["gridCol"]

for sub in stage_pos['subpositions']:
for sub in stage_pos["subpositions"]:
values = []
for field in ['x', 'y', 'z']:
for field in ["x", "y", "z"]:
if sub[field] != 0:
values.append(sub[field])
if len(values) == 1:
new_dict[sub['stageName']] = values[0]
new_dict[sub["stageName"]] = values[0]
else:
new_dict[sub['stageName']] = values
new_dict[sub["stageName"]] = values

return new_dict

Expand All @@ -252,14 +262,18 @@ def _create_position_array(self, pos):

# intialize virtual zarr store and save it under positions
timepoints, channels, slices = self._get_dimensions(pos)
self.position_arrays[pos] = zarr.empty(shape=(timepoints, channels, slices, self.height, self.width),
chunks=(1, 1, 1, self.height, self.width),
dtype=self.dtype)
self.position_arrays[pos] = zarr.empty(
shape=(timepoints, channels, slices, self.height, self.width),
chunks=(1, 1, 1, self.height, self.width),
dtype=self.dtype,
)
# add all the images with this specific dimension. Will be blank images if dataset
# is incomplete
for p, t, c, z in self.coord_map.keys():
if p == pos:
self.position_arrays[pos][t, c, z, :, :] = self.get_image(pos, t, c, z)
self.position_arrays[pos][t, c, z, :, :] = self.get_image(
pos, t, c, z
)

def _set_dtype(self):
"""
Expand Down Expand Up @@ -297,12 +311,12 @@ def _get_dimensions(self, position):
if position != tup[0]:
continue
else:
if tup[1]+1 > t:
t = tup[1]+1
if tup[2]+1 > c:
c = tup[2]+1
if tup[3]+1 > z:
z = tup[3]+1
if tup[1] + 1 > t:
t = tup[1] + 1
if tup[2] + 1 > c:
c = tup[2] + 1
if tup[3] + 1 > z:
z = tup[3] + 1

return t, c, z

Expand All @@ -324,9 +338,15 @@ def get_image(self, p, t, c, z):
"""

coord_key = (p, t, c, z)
coord = self.coord_map[coord_key] # (file, page, offset)

return np.memmap(coord[0], dtype=self.dtype, mode='r', offset=coord[2], shape=(self.height, self.width))
coord = self.coord_map[coord_key] # (file, page, offset)

return np.memmap(
coord[0],
dtype=self.dtype,
mode="r",
offset=coord[2],
shape=(self.height, self.width),
)

def get_zarr(self, position):
"""
Expand Down
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