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support non-square shaped tiles #15

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support non-square shaped tiles #15

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5ea5e4c
support non-square shaped tiles
JulesScholler Dec 1, 2023
420ba50
correct an error where x and y shape were inverted
JulesScholler Dec 4, 2023
2d347c5
remove testing on 3.7 (non supported by few packages)
JulesScholler Dec 4, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ jobs:
strategy:
matrix:
os: [ubuntu-latest]
python-version: [3.7, 3.8, 3.9]
python-version: [3.8, 3.9]

steps:
- name: Checkout
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4 changes: 2 additions & 2 deletions examples/example_converter.py
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Expand Up @@ -15,7 +15,7 @@
# If you don't have any data to try on, you can run the 'example_create_synthetic_dataset.py' script

# We then parse this data using the parser:
tiles = paprica.tileParser(path=path, frame_size=2048)
tiles = paprica.tileParser(path=path, frame_size_h=2048, frame_size_v=2048)

# Next, we batch convert the data. Please refer to the original paper to understand and set correctly the
# conversion parameters. The parameters that do not appear below are automatically determined but can also be
Expand All @@ -27,6 +27,6 @@
)

# It is also possible to batch reconstruct data
tiles_tiff = paprica.tileParser(path='path_to_tiff_data', frame_size=2048)
tiles_tiff = paprica.tileParser(path='path_to_tiff_data', frame_size_h=2048, frame_size_v=2048)
converter = paprica.tileConverter(tiles_tiff)
converter.batch_reconstruct_pixel()
2 changes: 1 addition & 1 deletion examples/example_segmentation.py
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Expand Up @@ -51,7 +51,7 @@ def compute_features(apr, parts):
# If you don't have any data to try on, you can run the 'example_create_synthetic_dataset.py' script

# We then parse this data using the parser
tiles = paprica.tileParser(path=path, frame_size=2048, ftype='apr')
tiles = paprica.tileParser(path=path, frame_size_h=2048, frame_size_v=2048, ftype='apr')

# Here we will manually train the segmenter on the first tile
trainer = paprica.tileTrainer(tiles[0, 0], func_to_compute_features=compute_features)
Expand Down
2 changes: 1 addition & 1 deletion examples/example_stitching.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
# If you don't have any data to try on, you can run the 'example_create_synthetic_dataset.py' script

# We then parse this data using the parser
tiles = paprica.tileParser(path=path, frame_size=2048, ftype='apr')
tiles = paprica.tileParser(path=path, frame_size_h=2048, frame_size_v=2048, ftype='apr')
# The previous parser expect the data to be in y_x.apr naming convention, this behavior can be adapted by creating
# your own parsing class that inherits from tileParser. We provide an example for COLM data where we just need to
# parse the data to associate each tile with its position on the grid:
Expand Down
3 changes: 2 additions & 1 deletion paprica/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,8 @@ def batch_convert_to_apr(self,
if self.is_multitile:
# Modify tileParser object to use APR instead
self.tiles = paprica.parser.tileParser(folder_apr,
frame_size=self.tiles.frame_size,
frame_size_h=self.tiles.frame_size_h,
frame_size_v=self.tiles.frame_size_v,
ftype='apr')

def batch_reconstruct_pixel(self, mode='constant', progress_bar=True):
Expand Down
34 changes: 24 additions & 10 deletions paprica/loader.py
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Expand Up @@ -46,7 +46,8 @@ def tile_from_apr(apr, parts):
neighbors=None,
neighbors_tot=None,
neighbors_path=None,
frame_size=2048,
frame_size_h=apr.shape(2),
frame_size_v=apr.shape(1),
folder_root=None,
channel=None)

Expand Down Expand Up @@ -76,7 +77,8 @@ def tile_from_path(path):
neighbors=None,
neighbors_tot=None,
neighbors_path=None,
frame_size=2048,
frame_size_h=2048,
frame_size_v=2048,
folder_root=os.path.basename(path),
channel=None)

Expand All @@ -86,7 +88,16 @@ class tileLoader():
Class to load each tile, neighboring tiles, segmentation and neighboring segmentation.

"""
def __init__(self, path, row, col, ftype, neighbors, neighbors_tot, neighbors_path, frame_size, folder_root,
def __init__(self, path,
row,
col,
ftype,
neighbors,
neighbors_tot,
neighbors_path,
frame_size_h,
frame_size_v,
folder_root,
channel):
"""
Constructor of tileLoader object.
Expand Down Expand Up @@ -131,8 +142,10 @@ def __init__(self, path, row, col, ftype, neighbors, neighbors_tot, neighbors_pa
in this case neighbors_tot = [[0, 0], [0, 2], [1, 1]]
neighbors_path: list
path of the neighbors whose coordinates are stored in neighbors
frame_size: int
camera frame size (only square sensors are supported for now).
frame_size_h: int
horizontal camera frame size.
frame_size_v: int
vertical camera frame size.
folder_root: str
root folder where everything should be saved.
channel: int
Expand All @@ -147,7 +160,8 @@ def __init__(self, path, row, col, ftype, neighbors, neighbors_tot, neighbors_pa
self.neighbors = neighbors
self.neighbors_tot = neighbors_tot
self.neighbors_path = neighbors_path
self.frame_size = frame_size
self.frame_size_h = frame_size_h
self.frame_size_v = frame_size_v
self.folder_root = folder_root
self.channel = channel
self.is_loaded = False
Expand Down Expand Up @@ -373,7 +387,7 @@ def _load_data(self, path):
elif self.type == 'clearscope':
u = self._load_clearscope(path)
elif self.type == 'tiff3D':
u = imread(path)
u = np.squeeze(imread(path))
elif self.type == 'apr':
apr = pyapr.APR()
parts = pyapr.ShortParticles()
Expand Down Expand Up @@ -401,7 +415,7 @@ def _load_raw(self, path):
numpy array containing the data.
"""
u = np.fromfile(path, dtype='uint16', count=-1)
return u.reshape((-1, self.frame_size, self.frame_size))
return u.reshape((-1, self.frame_size_v, self.frame_size_h))

def _load_colm(self, path):
"""
Expand All @@ -419,7 +433,7 @@ def _load_colm(self, path):
"""
files_sorted = sorted(glob(os.path.join(path, '*CHN0' + str(self.channel) + '_*tif')))
n_files = len(files_sorted)
v = np.empty((n_files, self.frame_size, self.frame_size), dtype='uint16')
v = np.empty((n_files, self.frame_size_v, self.frame_size_h), dtype='uint16')
for i, f in enumerate(tqdm(files_sorted, desc='Loading sequence', leave=False)):
v[i] = imread(f)
return v
Expand All @@ -440,7 +454,7 @@ def _load_clearscope(self, path):
"""
files_sorted = sorted(glob(os.path.join(path, '*')))
n_files = len(files_sorted)
v = np.empty((n_files, self.frame_size, self.frame_size), dtype='uint16')
v = np.empty((n_files, self.frame_size_v, self.frame_size_h), dtype='uint16')
for i, f in enumerate(tqdm(files_sorted, desc='Loading sequence', leave=False)):
v[i] = imread(f)

Expand Down
45 changes: 29 additions & 16 deletions paprica/parser.py
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Expand Up @@ -99,22 +99,25 @@ class baseParser():
Class used to parse several independent tiles (not multitile).

"""
def __init__(self, path, frame_size, ftype, verbose=True):
def __init__(self, path, frame_size_h, frame_size_v, ftype, verbose=True):
"""
Constructor of the baseParser object.

Parameters
----------
path: string
path where to look for the data.
frame_size: int
size of each frame (camera resolution).
frame_size_h: int
horizontal camera frame size.
frame_size_v: int
vertical camera frame size.
ftype: string
input data type in 'apr', 'tiff2D' or 'tiff3D'

"""
self.path = path
self.frame_size = frame_size
self.frame_size_h = frame_size_h
self.frame_size_v = frame_size_v
self.type = ftype
self.channel = None
self.tiles_list = self._get_tile_list()
Expand Down Expand Up @@ -403,7 +406,8 @@ def __getitem__(self, item):
neighbors=self.neighbors,
neighbors_tot=self.neighbors_tot,
neighbors_path=self.neighbors_path,
frame_size=self.frame_size,
frame_size_h=self.frame_size_h,
frame_size_v=self.frame_size_v,
folder_root=self.folder_root,
channel=self.channel)

Expand All @@ -429,7 +433,8 @@ def __iter__(self):
neighbors=self.neighbors,
neighbors_tot=self.neighbors_tot,
neighbors_path=self.neighbors_path,
frame_size=self.frame_size,
frame_size_h=self.frame_size_h,
frame_size_v=self.frame_size_v,
folder_root=self.folder_root,
channel=self.channel)

Expand All @@ -447,23 +452,26 @@ class tileParser(baseParser):
stitched later on.

"""
def __init__(self, path, frame_size=2048, ftype=None, verbose=True):
def __init__(self, path, frame_size_h=2048, frame_size_v=2048, ftype=None, verbose=True):
"""
Constructor of the tileParser object.

Parameters
----------
path: string
path where to look for the data.
frame_size: int
size of each frame (camera resolution).
frame_size_h: int
horizontal camera frame size.
frame_size_v: int
vertical camera frame size.
ftype: string
input data type in 'apr', 'tiff2D' or 'tiff3D'

"""

self.path = path
self.frame_size = frame_size
self.frame_size_h = frame_size_h
self.frame_size_v = frame_size_v
self.channel = None
if ftype is None:
self.type = self._get_type()
Expand Down Expand Up @@ -602,7 +610,8 @@ def __getitem__(self, item):
neighbors=neighbors,
neighbors_tot=neighbors_tot,
neighbors_path=neighbors_path,
frame_size=self.frame_size,
frame_size_h=self.frame_size_h,
frame_size_v=self.frame_size_v,
folder_root=self.folder_root,
channel=self.channel)

Expand All @@ -626,7 +635,8 @@ def __getitem__(self, item):
neighbors=neighbors,
neighbors_tot=neighbors_tot,
neighbors_path=neighbors_path,
frame_size=self.frame_size,
frame_size_h=self.frame_size_h,
frame_size_v=self.frame_size_v,
folder_root=self.folder_root,
channel=self.channel)

Expand Down Expand Up @@ -665,7 +675,8 @@ def __iter__(self):
neighbors=neighbors,
neighbors_tot=neighbors_tot,
neighbors_path=neighbors_path,
frame_size=self.frame_size,
frame_size_h=self.frame_size_h,
frame_size_v=self.frame_size_v,
folder_root=self.folder_root,
channel=self.channel)

Expand Down Expand Up @@ -712,7 +723,7 @@ def __init__(self, path, channel=0, verbose=True):
self.ncol = u.shape[1]
self.nrow = u.shape[0]
path = os.path.join(path, 'VW0')
super().__init__(path, frame_size=2048, ftype='colm', verbose=verbose)
super().__init__(path, frame_size_h=2048, frame_size_v=2048, ftype='colm', verbose=verbose)

self.channel = channel

Expand Down Expand Up @@ -832,7 +843,8 @@ def __init__(self, path, channel=0, verbose=True):
self.channel = channel
self.folder_settings, self.name_acq = os.path.split(path)
self._parse_settings()
self.frame_size = 2048
self.frame_size_h = 2048
self.frame_size_v = 2048
self.type = 'clearscope'
self.tiles_list = self._get_tile_list()
self.n_tiles = len(self.tiles_list)
Expand Down Expand Up @@ -1074,7 +1086,8 @@ def _get_n_channels(path):
# """
#
# self.path = path
# self.frame_size = 2048
# self.frame_size_h = 2048
# self.frame_size_v = 2048
# self.channel = channel
# self.channel_wavelength = self._get_channel_wavelength(channel)
# self.type = 'mesospim'
Expand Down
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