def __getitem__(self, index):
section_name = self.sections[index]
direction, number = section_name.split(sep="_")
if direction == "i":
im = self.seismic[int(number), :, :, :]
lbl = self.labels[int(number), :, :]
elif direction == "x":
im = self.seismic[:, :, int(number), :]
lbl = self.labels[:, int(number), :]
im = np.swapaxes(im, 0, 1) # From WCH to CWH
im, lbl = _transform_WH_to_HW(im), _transform_WH_to_HW(lbl)
# dump images before augmentation
if self.debug:
outdir = f"debug/testSectionLoaderWithDepth_{self.split}_raw"
generate_path(outdir)
# this needs to take the first dimension of image (no depth) but lbl only has 1 dim
path_prefix = f"{outdir}/index_{index}_section_{section_name}"
image_to_disk(im[0, :, :], path_prefix + "_img.png")
mask_to_disk(lbl, path_prefix + "_lbl.png", self.n_classes)
if self.augmentations is not None:
im = _transform_CHW_to_HWC(im)
augmented_dict = self.augmentations(image=im, mask=lbl)
im, lbl = augmented_dict["image"], augmented_dict["mask"]
im = _transform_HWC_to_CHW(im)
if self.is_transform:
im, lbl = self.transform(im, lbl)
# dump images and labels to disk after augmentation
if self.debug:
outdir = (
f"debug/testSectionLoaderWithDepth_{self.split}_{'aug' if self.augmentations is not None else 'noaug'}"
)
generate_path(outdir)
path_prefix = f"{outdir}/index_{index}_section_{section_name}"
image_to_disk(np.array(im[0, :, :]), path_prefix + "_img.png")
mask_to_disk(np.array(lbl[0, :, :]), path_prefix + "_lbl.png",
self.n_classes)
return im, lbl
def __getitem__(self, index):
patch_name = self.patches[index]
direction, idx, xdx, ddx = patch_name.split(sep="_")
# Shift offsets the padding that is added in training
# shift = self.patch_size if "test" not in self.split else 0
# Remember we are cancelling the shift since we no longer pad
shift = 0
idx, xdx, ddx = int(idx) + shift, int(xdx) + shift, int(ddx) + shift
if direction == "i":
im = self.seismic[idx, :, xdx:xdx + self.patch_size,
ddx:ddx + self.patch_size]
lbl = self.labels[idx, xdx:xdx + self.patch_size,
ddx:ddx + self.patch_size]
elif direction == "x":
im = self.seismic[idx:idx + self.patch_size, :, xdx,
ddx:ddx + self.patch_size]
lbl = self.labels[idx:idx + self.patch_size, xdx,
ddx:ddx + self.patch_size]
im = np.swapaxes(im, 0, 1) # From WCH to CWH
im, lbl = _transform_WH_to_HW(im), _transform_WH_to_HW(lbl)
if self.augmentations is not None:
im = _transform_CHW_to_HWC(im)
augmented_dict = self.augmentations(image=im, mask=lbl)
im, lbl = augmented_dict["image"], augmented_dict["mask"]
im = _transform_HWC_to_CHW(im)
# dump images and labels to disk
if self.debug:
outdir = f"patchLoaderWithSectionDepth_{self.split}_{'aug' if self.augmentations is not None else 'noaug'}"
generate_path(outdir)
image_to_disk(im[0, :, :], f"{outdir}/{index}_img.png")
mask_to_disk(lbl, f"{outdir}/{index}_lbl.png")
if self.is_transform:
im, lbl = self.transform(im, lbl)
return im, lbl
def __getitem__(self, index):
patch_name = self.patches[index]
direction, idx, xdx, ddx = patch_name.split(sep="_")
# Shift offsets the padding that is added in training
# shift = self.patch_size if "test" not in self.split else 0
# Remember we are cancelling the shift since we no longer pad
shift = 0
idx, xdx, ddx = int(idx) + shift, int(xdx) + shift, int(ddx) + shift
if direction == "i":
im = self.seismic[idx, xdx:xdx + self.patch_size,
ddx:ddx + self.patch_size]
lbl = self.labels[idx, xdx:xdx + self.patch_size,
ddx:ddx + self.patch_size]
elif direction == "x":
im = self.seismic[idx:idx + self.patch_size, xdx,
ddx:ddx + self.patch_size]
lbl = self.labels[idx:idx + self.patch_size, xdx,
ddx:ddx + self.patch_size]
im, lbl = _transform_WH_to_HW(im), _transform_WH_to_HW(lbl)
# dump raw images before augmentation
if self.debug:
outdir = f"debug/patchLoader_{self.split}_raw"
generate_path(outdir)
path_prefix = f"{outdir}/index_{index}_section_{patch_name}"
image_to_disk(im, path_prefix + "_img.png")
mask_to_disk(lbl, path_prefix + "_lbl.png", self.n_classes)
if self.augmentations is not None:
augmented_dict = self.augmentations(image=im, mask=lbl)
im, lbl = augmented_dict["image"], augmented_dict["mask"]
# dump images and labels to disk
if self.debug:
outdir = f"patchLoader_{self.split}_{'aug' if self.augmentations is not None else 'noaug'}"
generate_path(outdir)
path_prefix = f"{outdir}/{index}"
image_to_disk(im, path_prefix + "_img.png")
mask_to_disk(lbl, path_prefix + "_lbl.png", self.n_classes)
if self.is_transform:
im, lbl = self.transform(im, lbl)
# dump images and labels to disk
if self.debug:
outdir = f"debug/patchLoader_{self.split}_{'aug' if self.augmentations is not None else 'noaug'}"
generate_path(outdir)
path_prefix = f"{outdir}/index_{index}_section_{patch_name}"
image_to_disk(np.array(im[0, :, :]), path_prefix + "_img.png")
mask_to_disk(np.array(lbl[0, :, :]), path_prefix + "_lbl.png",
self.n_classes)
return im, lbl
def __getitem__(self, index):
section_name = self.sections[index]
direction, number = section_name.split(sep="_")
if direction == "i":
im = self.seismic[int(number), :, :]
lbl = self.labels[int(number), :, :]
elif direction == "x":
im = self.seismic[:, int(number), :]
lbl = self.labels[:, int(number), :]
im, lbl = _transform_WH_to_HW(im), _transform_WH_to_HW(lbl)
if self.debug and "test" in self.split:
outdir = f"debug/sectionLoader_{self.split}_raw"
generate_path(outdir)
path_prefix = f"{outdir}/index_{index}_section_{section_name}"
image_to_disk(im, path_prefix + "_img.png")
mask_to_disk(lbl, path_prefix + "_lbl.png", self.n_classes)
if self.augmentations is not None:
augmented_dict = self.augmentations(image=im, mask=lbl)
im, lbl = augmented_dict["image"], augmented_dict["mask"]
if self.is_transform:
im, lbl = self.transform(im, lbl)
if self.debug and "test" in self.split:
outdir = f"debug/sectionLoader_{self.split}_{'aug' if self.augmentations is not None else 'noaug'}"
generate_path(outdir)
path_prefix = f"{outdir}/index_{index}_section_{section_name}"
image_to_disk(np.array(im[0]), path_prefix + "_img.png")
mask_to_disk(np.array(lbl[0]), path_prefix + "_lbl.png",
self.n_classes)
return im, lbl
def _patch_label_2d(
model,
img,
pre_processing,
output_processing,
patch_size,
stride,
batch_size,
device,
num_classes,
split,
debug,
MIN,
MAX,
):
"""Processes a whole section
"""
img = torch.squeeze(img)
h, w = img.shape[-2], img.shape[-1] # height and width
# Pad image with patch_size/2:
ps = int(np.floor(patch_size / 2)) # pad size
img_p = F.pad(img, pad=(ps, ps, ps, ps), mode="constant", value=0)
output_p = torch.zeros([1, num_classes, h + 2 * ps, w + 2 * ps])
# generate output:
for batch_indexes in _generate_batches(h,
w,
ps,
patch_size,
stride,
batch_size=batch_size):
batch = torch.stack(
[
pipe(
img_p,
_extract_patch(hdx, wdx, ps, patch_size),
pre_processing,
) for hdx, wdx in batch_indexes
],
dim=0,
)
model_output = model(batch.to(device))
for (hdx, wdx), output in zip(batch_indexes,
model_output.detach().cpu()):
output = output_processing(output)
output_p[:, :, hdx + ps:hdx + ps + patch_size,
wdx + ps:wdx + ps + patch_size, ] += output
# dump the data right before it's being put into the model and after scoring
if debug:
outdir = f"debug/test/batch_{split}"
generate_path(outdir)
for i in range(batch.shape[0]):
path_prefix = f"{outdir}/{batch_indexes[i][0]}_{batch_indexes[i][1]}"
model_output = model_output.detach().cpu()
# save image:
image_to_disk(np.array(batch[i, 0, :, :]),
path_prefix + "_img.png", MIN, MAX)
# dump model prediction:
mask_to_disk(model_output[i, :, :, :].argmax(dim=0).numpy(),
path_prefix + "_pred.png", num_classes)
# dump model confidence values
for nclass in range(num_classes):
image_to_disk(model_output[i, nclass, :, :].numpy(),
path_prefix + f"_class_{nclass}_conf.png",
MIN, MAX)
# crop the output_p in the middle
output = output_p[:, :, ps:-ps, ps:-ps]
return output