Created
January 19, 2022 17:23
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This is a code for creating a custom transform where I am reading a list of images and converting to a single image
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import monai | |
import inspect | |
from monai.transforms import LoadImage, AddChannel, Compose | |
import json | |
from typing import Dict, List, Optional, Sequence, Union | |
from monai.transforms import Transform | |
from monai.data.image_reader import ImageReader, ITKReader, NibabelReader, NumpyReader, PILReader | |
import logging | |
import warnings | |
from monai.config import DtypeLike, PathLike | |
import os | |
from PIL import Image | |
import numpy as np | |
from pathlib import Path | |
from monai.utils import InterpolateMode, OptionalImportError, ensure_tuple, look_up_option, optional_import | |
SUPPORTED_READERS = { | |
"itkreader": ITKReader, | |
"numpyreader": NumpyReader, | |
"pilreader": PILReader, | |
"nibabelreader": NibabelReader, | |
} | |
class LoadImageList(Transform): | |
""" | |
In this transform we are reading a list of images and converting them to a single image by tiling. | |
I will ideally like to overload the LoadImage Transform. But for the moment I reused the reader functionality from | |
LoadImage. | |
""" | |
def __init__(self, reader=None, image_only: bool = False, | |
dtype: DtypeLike = np.float32, *args, **kwargs): | |
self.auto_select = reader is None | |
self.image_only = image_only | |
self.dtype = dtype | |
self.readers: List[ImageReader] = [] | |
for r in SUPPORTED_READERS: # set predefined readers as default | |
try: | |
self.register(SUPPORTED_READERS[r](*args, **kwargs)) | |
except OptionalImportError: | |
logging.getLogger(self.__class__.__name__).debug( | |
f"required package for reader {r} is not installed, or the version doesn't match requirement." | |
) | |
except TypeError: # the reader doesn't have the corresponding args/kwargs | |
logging.getLogger(self.__class__.__name__).debug( | |
f"{r} is not supported with the given parameters {args} {kwargs}." | |
) | |
self.register(SUPPORTED_READERS[r]()) | |
if reader is None: | |
return # no user-specified reader, no need to register | |
for _r in ensure_tuple(reader): | |
if isinstance(_r, str): | |
the_reader = look_up_option(_r.lower(), SUPPORTED_READERS) | |
try: | |
self.register(the_reader(*args, **kwargs)) | |
except OptionalImportError: | |
warnings.warn( | |
f"required package for reader {r} is not installed, or the version doesn't match requirement." | |
) | |
except TypeError: # the reader doesn't have the corresponding args/kwargs | |
warnings.warn(f"{r} is not supported with the given parameters {args} {kwargs}.") | |
self.register(the_reader()) | |
elif inspect.isclass(_r): | |
self.register(_r(*args, **kwargs)) | |
else: | |
self.register(_r) # reader instance, ignoring the constructor args/kwargs | |
return | |
def register(self, reader: ImageReader): | |
""" | |
Register image reader to load image file and meta data. | |
Args: | |
reader: reader instance to be registered with this loader. | |
""" | |
if not isinstance(reader, ImageReader): | |
warnings.warn(f"Preferably the reader should inherit ImageReader, but got {type(reader)}.") | |
self.readers.append(reader) | |
def __call__(self, filename_list = None, | |
reader: Optional[ImageReader] = None): | |
self.imageList = [] | |
for filename in filename_list: | |
filename = tuple(f"{Path(s).expanduser()}" for s in ensure_tuple(filename)) # allow Path objects | |
img = None | |
if reader is not None: | |
img = reader.read(filename) # runtime specified reader | |
self.imageList.append(img) | |
else: | |
for reader in self.readers[::-1]: | |
if self.auto_select: # rely on the filename extension to choose the reader | |
if reader.verify_suffix(filename): | |
img = reader.read(filename) | |
self.imageList.append(img) | |
break | |
else: # try the user designated readers | |
try: | |
img = reader.read(filename) | |
self.imageList.append(img) | |
except Exception as e: | |
logging.getLogger(self.__class__.__name__).debug( | |
f"{reader.__class__.__name__}: unable to load {filename}.\n" f"Error: {e}" | |
) | |
else: | |
break | |
image_np = self.createtile(reader) | |
return image_np | |
def createtile(self, reader): | |
""" | |
In this function we are taking a list of 4 numpy arrays (images), and converting them to a single image where | |
the images will be tiled in 2X2 fashion. This is achieved through a concatenation process. We have hard coaded it at the moment | |
where there are 4 images of size (224, 224) leading to an image of size (448, 448) | |
""" | |
# imagesize is (224, 224) and in | |
image_np = np.empty((448, 448)) | |
_img = self.imageList[0] | |
img_array, meta_data = reader.get_data(_img) | |
img_array = img_array.astype(self.dtype, copy=False) | |
image_np[0:224, 0:224] = img_array | |
_img = self.imageList[1] | |
img_array, meta_data = reader.get_data(_img) | |
img_array = img_array.astype(self.dtype, copy=False) | |
image_np[0:224, 224:448] = img_array | |
_img = self.imageList[2] | |
img_array, meta_data = reader.get_data(_img) | |
img_array = img_array.astype(self.dtype, copy=False) | |
image_np[224:448, 0:224] = img_array | |
_img = self.imageList[3] | |
img_array, meta_data = reader.get_data(_img) | |
img_array = img_array.astype(self.dtype, copy=False) | |
image_np[224:448, 224:448] = img_array | |
return image_np | |
def main(): | |
listOfImages = ['filename1', 'filename2', 'filename3', 'filename4'] | |
#This works | |
image_array = LoadImageList()(listOfImages) | |
#This does not work | |
transform = Compose([LoadImageList()]) | |
img_array = transform(listOfImages) | |
if __name__ == '__main__': | |
main() |
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