def predict_whole_volume_by_tiling(log, sessionTf, cnn3d, channels, roi_mask,
batchsize, save_fms_flag, idxs_fms_to_save):
# One of the main routines. Segment whole volume tile-by-tile.
# Receptive field is list [size-x, size-y, size-z]. -1 to exclude the central voxel.
half_rec_field = [(cnn3d.recFieldCnn[i] - 1) // 2
for i in range(len(cnn3d.recFieldCnn))]
# For tiling the volume: Stride is how much I move in each dimension to get the next tile.
# I stride exactly the number of voxels that are predicted per forward pass.
n_voxels_predicted = cnn3d.finalTargetLayer.outputShape["test"][2:]
stride_of_tiling = n_voxels_predicted # [str-x, str-y, str-z]
# Find the total number of feature maps that will be created:
# NOTE: save_fms_flag should contain an entry per pathwayType, even if just [].
# If not [], the list should contain one entry per layer of the pathway, even if just [].
# The layer entries, if not [], they should have to integers, lower and upper FM to visualise.
n_fms_to_save = calc_num_fms_to_save(
cnn3d.pathways, idxs_fms_to_save) if save_fms_flag else 0
# Arrays that will be returned.
inp_chan_dims = list(
channels.shape[1:]) # Dimensions of (padded) input channels.
# The main output. Predicted probability-maps for the whole volume, one per class.
# Will be constructed by stitching together the predictions from each tile.
prob_maps_vols = np.zeros([cnn3d.num_classes] + inp_chan_dims,
dtype="float32")
# create the big array that will hold all the fms (for feature extraction).
array_fms_to_save = np.zeros([n_fms_to_save] + inp_chan_dims,
dtype="float32") if save_fms_flag else None
# Tile the image and get all slices of the tiles that it fully breaks down to.
slice_coords_all_tiles = get_slice_coords_of_all_img_tiles(
log, cnn3d.pathways[0].getShapeOfInput("test")[2:], stride_of_tiling,
batchsize, inp_chan_dims, roi_mask)
n_tiles_for_subj = len(slice_coords_all_tiles)
log.print3("Ready to make predictions for all image segments (parts).")
log.print3("Total number of Segments to process:" + str(n_tiles_for_subj))
idx_next_tile_in_pred_vols = 0
idx_next_tile_in_fm_vols = 0
n_batches = n_tiles_for_subj // batchsize
t_fwd_pass_subj = 0 # time it took for forward pass over all tiles of subject.
for batch_i in range(n_batches):
print_progress_step(log, n_batches, batch_i, batchsize,
n_tiles_for_subj)
# Extract data for the segments of this batch.
# ( I could modularize extractDataOfASegmentFromImagesUsingSampledSliceCoords()
# of training and use it here as well. )
slice_coords_of_tiles_batch = slice_coords_all_tiles[batch_i *
batchsize:
(batch_i + 1) *
batchsize]
channs_of_tiles_per_path = extractSegmentsGivenSliceCoords(
cnn3d, slice_coords_of_tiles_batch, channels, cnn3d.recFieldCnn)
# ============================== Perform forward pass ====================================
t_fwd_start = time.time()
ops_to_fetch = cnn3d.get_main_ops('test')
list_of_ops = [ops_to_fetch['pred_probs']
] + ops_to_fetch['list_of_fms_per_layer']
feeds_dict = prepare_feeds_dict(cnn3d.get_main_feeds('test'),
channs_of_tiles_per_path)
# Forward pass
out_val_of_ops = sessionTf.run(fetches=list_of_ops,
feed_dict=feeds_dict)
prob_maps_batch = out_val_of_ops[0]
fms_per_layer_and_path_for_batch = out_val_of_ops[
1:] # [] if no FMs specified.
t_fwd_pass_subj += time.time() - t_fwd_start
# ================ Construct probability maps (volumes) by Stitching ====================
# Stitch predictions for tiles of this batch, to create the probability maps for whole volume.
# Each prediction for a tile needs to be placed in the correct location in the volume.
(idx_next_tile_in_pred_vols,
prob_maps_vols) = stitch_predicted_to_prob_maps(
prob_maps_vols, idx_next_tile_in_pred_vols, prob_maps_batch,
batchsize, slice_coords_all_tiles, half_rec_field,
stride_of_tiling)
# ============== Construct feature maps (volumes) by Stitching =====================
if save_fms_flag:
(idx_next_tile_in_fm_vols,
array_fms_to_save) = stitch_predicted_to_fms(
array_fms_to_save, idx_next_tile_in_fm_vols,
fms_per_layer_and_path_for_batch, batchsize,
slice_coords_all_tiles, half_rec_field, stride_of_tiling,
n_voxels_predicted, cnn3d.pathways, idxs_fms_to_save)
# Done with batch
log.print3("TIMING: Segmentation of subject: [Forward Pass:] {0:.2f}".
format(t_fwd_pass_subj) + " secs.")
return prob_maps_vols, array_fms_to_save
def inferenceWholeVolumes(
sessionTf,
cnn3d,
log,
val_or_test,
savePredictedSegmAndProbsDict,
listOfFilepathsToEachChannelOfEachPatient,
providedGtLabelsBool, #boolean. DSC calculation will be performed if this is provided.
listOfFilepathsToGtLabelsOfEachPatient,
providedRoiMaskForFastInfBool,
listOfFilepathsToRoiMaskFastInfOfEachPatient,
namesForSavingSegmAndProbs,
suffixForSegmAndProbsDict,
# Hyper parameters
batchsize,
#----Preprocessing------
padInputImagesBool,
#--------For FM visualisation---------
saveIndividualFmImagesForVisualisation,
saveMultidimensionalImageWithAllFms,
indicesOfFmsToVisualisePerPathwayTypeAndPerLayer,
namesForSavingFms):
# saveIndividualFmImagesForVisualisation: should contain an entry per pathwayType, even if just []...
# ... If not [], the list should contain one entry per layer of the pathway, even if just [].
# ... The layer entries, if not [], they should have to integers, lower and upper FM to visualise. Excluding the highest index.
validation_or_testing_str = "Validation" if val_or_test == "val" else "Testing"
log.print3(
"###########################################################################################################"
)
log.print3("############################# Starting full Segmentation of " +
str(validation_or_testing_str) +
" subjects ##########################")
log.print3(
"###########################################################################################################"
)
start_time = time.time()
NA_PATTERN = AccuracyOfEpochMonitorSegmentation.NA_PATTERN
NUMBER_OF_CLASSES = cnn3d.num_classes
total_number_of_images = len(listOfFilepathsToEachChannelOfEachPatient)
#one dice score for whole + for each class)
# A list of dimensions: total_number_of_images X NUMBER_OF_CLASSES
diceCoeffs1 = [[-1] * NUMBER_OF_CLASSES
for i in range(total_number_of_images)
] #AllpredictedLes/AllLesions
diceCoeffs2 = [[-1] * NUMBER_OF_CLASSES
for i in range(total_number_of_images)
] #predictedInsideRoiMask/AllLesions
diceCoeffs3 = [
[-1] * NUMBER_OF_CLASSES for i in range(total_number_of_images)
] #predictedInsideRoiMask/ LesionsInsideRoiMask (for comparisons)
recFieldCnn = cnn3d.recFieldCnn
#stride is how much I move in each dimension to acquire the next imagePart.
#I move exactly the number I segment in the centre of each image part (originally this was 9^3 segmented per imagePart).
numberOfCentralVoxelsClassified = cnn3d.finalTargetLayer.outputShape[
"test"][2:]
strideOfImagePartsPerDimensionInVoxels = numberOfCentralVoxelsClassified
rczHalfRecFieldCnn = [(recFieldCnn[i] - 1) // 2 for i in range(3)]
#Find the total number of feature maps that will be created:
#NOTE: saveIndividualFmImagesForVisualisation should contain an entry per pathwayType, even if just []. If not [], the list should contain one entry per layer of the pathway, even if just []. The layer entries, if not [], they should have to integers, lower and upper FM to visualise.
if saveIndividualFmImagesForVisualisation or saveMultidimensionalImageWithAllFms:
totalNumberOfFMsToProcess = 0
for pathway in cnn3d.pathways:
indicesOfFmsToVisualisePerLayerOfCertainPathway = indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[
pathway.pType()]
if indicesOfFmsToVisualisePerLayerOfCertainPathway != []:
for layer_i in range(len(pathway.getLayers())):
indicesOfFmsToVisualiseForCertainLayerOfCertainPathway = indicesOfFmsToVisualisePerLayerOfCertainPathway[
layer_i]
if indicesOfFmsToVisualiseForCertainLayerOfCertainPathway!=[] :
#If the user specifies to grab more feature maps than exist (eg 9999), correct it, replacing it with the number of FMs in the layer.
numberOfFeatureMapsInThisLayer = pathway.getLayer(
layer_i).getNumberOfFeatureMaps()
indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[
1] = min(
indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[
1], numberOfFeatureMapsInThisLayer)
totalNumberOfFMsToProcess += indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[
1] - indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[
0]
for image_i in range(total_number_of_images):
log.print3(
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
)
log.print3("~~~~~~~~~~~~~~~~~~~~ Segmenting subject with index #" +
str(image_i) + " ~~~~~~~~~~~~~~~~~~~~")
#load the image channels in cpu
[
imageChannels,
gtLabelsImage, #only for accurate/correct DICE1-2 calculation
roiMask,
arrayWithWeightMapsWhereToSampleForEachCategory, #only used in training. Placeholder here.
tupleOfPaddingPerAxesLeftRight #( (padLeftR, padRightR), (padLeftC,padRightC), (padLeftZ,padRightZ)). All 0s when no padding.
] = load_imgs_of_subject(
log,
None,
"test",
False, # run_input_checks.
image_i,
listOfFilepathsToEachChannelOfEachPatient,
providedGtLabelsBool,
listOfFilepathsToGtLabelsOfEachPatient,
cnn3d.num_classes,
False, # providedWeightMapsToSampleForEachCategory
None,
providedRoiMaskForFastInfBool,
listOfFilepathsToRoiMaskFastInfOfEachPatient,
padInputImagesBool,
recFieldCnn, # only used if padInputsBool
cnn3d.pathways[0].getShapeOfInput("test")[
2:] # dimsOfPrimeSegmentRcz, for padding
)
niiDimensions = list(imageChannels.shape[1:])
#The predicted probability-maps for the whole volume, one per class. Will be constructed by stitching together the predictions from each segment.
predProbMapsPerClass = np.zeros([NUMBER_OF_CLASSES] + niiDimensions,
dtype="float32")
#create the big array that will hold all the fms (for feature extraction, to save as a big multi-dim image).
if saveIndividualFmImagesForVisualisation or saveMultidimensionalImageWithAllFms:
multidimensionalImageWithAllToBeVisualisedFmsArray = np.zeros(
[totalNumberOfFMsToProcess] + niiDimensions, dtype="float32")
# Tile the image and get all slices of the segments that it fully breaks down to.
[sliceCoordsOfSegmentsInImage] = getCoordsOfAllSegmentsOfAnImage(
log,
cnn3d.pathways[0].getShapeOfInput("test")
[2:], # dimsOfPrimarySegment
strideOfImagePartsPerDimensionInVoxels,
batchsize,
imageChannels,
roiMask)
log.print3(
"Starting to segment each image-part by calling the cnn.cnnTestModel(i). This part takes a few mins per volume..."
)
num_segments_for_case = len(sliceCoordsOfSegmentsInImage)
log.print3("Total number of Segments to process:" +
str(num_segments_for_case))
imagePartOfConstructedProbMap_i = 0
imagePartOfConstructedFeatureMaps_i = 0
num_batches = num_segments_for_case // batchsize
extractTimePerSubject = 0
loadingTimePerSubject = 0
fwdPassTimePerSubject = 0
for batch_i in range(num_batches):
print_progress_step = max(1, num_batches // 5)
if batch_i == 0 or ((batch_i + 1) % print_progress_step) == 0 or (
batch_i + 1) == num_batches:
log.print3("Processed " + str((batch_i + 1) * batchsize) +
"/" + str(num_segments_for_case) + " segments.")
# Extract the data for the segments of this batch. ( I could modularize extractDataOfASegmentFromImagesUsingSampledSliceCoords() of training and use it here as well. )
start_extract_time = time.time()
sliceCoordsOfSegmentsInBatch = sliceCoordsOfSegmentsInImage[
batch_i * batchsize:(batch_i + 1) * batchsize]
[channsOfSegmentsPerPath
] = extractSegmentsGivenSliceCoords(cnn3d,
sliceCoordsOfSegmentsInBatch,
imageChannels, recFieldCnn)
end_extract_time = time.time()
extractTimePerSubject += end_extract_time - start_extract_time
# ======= Run the inference ============
ops_to_fetch = cnn3d.get_main_ops('test')
list_of_ops = [ops_to_fetch['pred_probs']
] + ops_to_fetch['list_of_fms_per_layer']
# No loading of data in bulk as in training, cause here it's only 1 batch per iteration.
start_loading_time = time.time()
feeds = cnn3d.get_main_feeds('test')
feeds_dict = {
feeds['x']: np.asarray(channsOfSegmentsPerPath[0],
dtype='float32')
}
for path_i in range(len(channsOfSegmentsPerPath[1:])):
feeds_dict.update({
feeds['x_sub_' + str(path_i)]:
np.asarray(channsOfSegmentsPerPath[1 + path_i],
dtype='float32')
})
end_loading_time = time.time()
loadingTimePerSubject += end_loading_time - start_loading_time
start_testing_time = time.time()
# Forward pass
# featureMapsOfEachLayerAndPredictionProbabilitiesAtEndForATestBatch = cnn3d.cnnTestAndVisualiseAllFmsFunction( *input_args_to_net )
featureMapsOfEachLayerAndPredictionProbabilitiesAtEndForATestBatch = sessionTf.run(
fetches=list_of_ops, feed_dict=feeds_dict)
end_testing_time = time.time()
fwdPassTimePerSubject += end_testing_time - start_testing_time
predictionForATestBatch = featureMapsOfEachLayerAndPredictionProbabilitiesAtEndForATestBatch[
0]
listWithTheFmsOfAllLayersSortedByPathwayTypeForTheBatch = featureMapsOfEachLayerAndPredictionProbabilitiesAtEndForATestBatch[
1:] # If no FMs visualised, this should return []
#No reshape needed, cause I now do it internally. But to dimensions (batchSize, FMs, R,C,Z).
#~~~~~~~~~~~~~~~~CONSTRUCT THE PREDICTED PROBABILITY MAPS~~~~~~~~~~~~~~
#From the results of this batch, create the prediction image by putting the predictions to the correct place in the image.
for imagePart_in_this_batch_i in range(batchsize):
#Now put the label-cube in the new-label-segmentation-image, at the correct position.
#The very first label goes not in index 0,0,0 but half-patch further away! At the position of the central voxel of the top-left patch!
sliceCoordsOfThisSegment = sliceCoordsOfSegmentsInImage[
imagePartOfConstructedProbMap_i]
coordsOfTopLeftVoxelForThisPart = [
sliceCoordsOfThisSegment[0][0],
sliceCoordsOfThisSegment[1][0],
sliceCoordsOfThisSegment[2][0]
]
predProbMapsPerClass[:, coordsOfTopLeftVoxelForThisPart[0] +
rczHalfRecFieldCnn[0]:
coordsOfTopLeftVoxelForThisPart[0] +
rczHalfRecFieldCnn[0] +
strideOfImagePartsPerDimensionInVoxels[0],
coordsOfTopLeftVoxelForThisPart[1] +
rczHalfRecFieldCnn[1]:
coordsOfTopLeftVoxelForThisPart[1] +
rczHalfRecFieldCnn[1] +
strideOfImagePartsPerDimensionInVoxels[1],
coordsOfTopLeftVoxelForThisPart[2] +
rczHalfRecFieldCnn[2]:
coordsOfTopLeftVoxelForThisPart[2] +
rczHalfRecFieldCnn[2] +
strideOfImagePartsPerDimensionInVoxels[2],
] = predictionForATestBatch[
imagePart_in_this_batch_i]
imagePartOfConstructedProbMap_i += 1
#~~~~~~~~~~~~~FINISHED CONSTRUCTING THE PREDICTED PROBABILITY MAPS~~~~~~~
#~~~~~~~~~~~~~~CONSTRUCT THE FEATURE MAPS FOR VISUALISATION~~~~~~~~~~~~~~~~~
if saveIndividualFmImagesForVisualisation or saveMultidimensionalImageWithAllFms:
fmsReturnedForATestBatchForCertainLayer = None
#currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray is the index in the multidimensional array that holds all the to-be-visualised-fms. It is the one that corresponds to the next to-be-visualised indexOfTheLayerInTheReturnedListByTheBatchTraining.
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray = 0
#indexOfTheLayerInTheReturnedListByTheBatchTraining is the index over all the layers in the returned list. I will work only with the ones specified to visualise.
indexOfTheLayerInTheReturnedListByTheBatchTraining = 0
for pathway in cnn3d.pathways:
for layer_i in range(len(pathway.getLayers())):
if indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[
pathway.pType(
)] == [] or indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[
pathway.pType()][layer_i] == []:
continue
indicesOfFmsToExtractFromThisLayer = indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[
pathway.pType()][layer_i]
fmsReturnedForATestBatchForCertainLayer = listWithTheFmsOfAllLayersSortedByPathwayTypeForTheBatch[
indexOfTheLayerInTheReturnedListByTheBatchTraining]
#We specify a range of fms to visualise from a layer. currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray : highIndexOfFmsInTheMultidimensionalImageToFillInThisIterationExcluding defines were to put them in the multidimensional-image-array.
highIndexOfFmsInTheMultidimensionalImageToFillInThisIterationExcluding = currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray + indicesOfFmsToExtractFromThisLayer[
1] - indicesOfFmsToExtractFromThisLayer[0]
fmImageInMultidimArrayToReconstructInThisIteration = multidimensionalImageWithAllToBeVisualisedFmsArray[
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray:
highIndexOfFmsInTheMultidimensionalImageToFillInThisIterationExcluding]
#=========================================================================================================================================
#====the following calculations could be move OUTSIDE THE FOR LOOPS, by using the kernel-size parameter (from the cnn instance) instead of the shape of the returned value.
#====fmsReturnedForATestBatchForCertainLayer.shape[2] - (numberOfCentralVoxelsClassified[0]-1) is essentially the width of the patch left after the convolutions.
#====These calculations are pathway and layer-specific. So they could be done once, prior to image processing, and results cached in a list to be accessed during the loop.
numberOfVoxToSubtrToGetPatchWidthAtThisFm_R = numberOfCentralVoxelsClassified[
0] - 1 if pathway.pType() != pt.SUBS else int(
math.ceil((numberOfCentralVoxelsClassified[0] *
1.0) / pathway.subsFactor()[0]) - 1)
numberOfVoxToSubtrToGetPatchWidthAtThisFm_C = numberOfCentralVoxelsClassified[
1] - 1 if pathway.pType() != pt.SUBS else int(
math.ceil((numberOfCentralVoxelsClassified[1] *
1.0) / pathway.subsFactor()[1]) - 1)
numberOfVoxToSubtrToGetPatchWidthAtThisFm_Z = numberOfCentralVoxelsClassified[
2] - 1 if pathway.pType() != pt.SUBS else int(
math.ceil((numberOfCentralVoxelsClassified[2] *
1.0) / pathway.subsFactor()[2]) - 1)
rPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions = fmsReturnedForATestBatchForCertainLayer.shape[
2] - numberOfVoxToSubtrToGetPatchWidthAtThisFm_R
cPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions = fmsReturnedForATestBatchForCertainLayer.shape[
3] - numberOfVoxToSubtrToGetPatchWidthAtThisFm_C
zPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions = fmsReturnedForATestBatchForCertainLayer.shape[
4] - numberOfVoxToSubtrToGetPatchWidthAtThisFm_Z
rOfTopLeftCentralVoxelAtTheFm = (
rPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions
- 1
) // 2 #-1 so that if width is even, I'll get the left voxel from the centre as 1st, which I THINK is how I am getting the patches from the original image.
cOfTopLeftCentralVoxelAtTheFm = (
cPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions
- 1) // 2
zOfTopLeftCentralVoxelAtTheFm = (
zPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions
- 1) // 2
#the math.ceil / subsamplingFactor is a trick to make it work for even subsamplingFactor too. Eg 9/2=4.5 => Get 5. Combined with the trick at repeat, I get my correct number of central voxels hopefully.
numberOfCentralVoxelsToGetInDirectionR = int(
math.ceil(
(numberOfCentralVoxelsClassified[0] * 1.0) /
pathway.subsFactor()[0])
) if pathway.pType(
) == pt.SUBS else numberOfCentralVoxelsClassified[0]
numberOfCentralVoxelsToGetInDirectionC = int(
math.ceil(
(numberOfCentralVoxelsClassified[1] * 1.0) /
pathway.subsFactor()[1])
) if pathway.pType(
) == pt.SUBS else numberOfCentralVoxelsClassified[1]
numberOfCentralVoxelsToGetInDirectionZ = int(
math.ceil(
(numberOfCentralVoxelsClassified[2] * 1.0) /
pathway.subsFactor()[2])
) if pathway.pType(
) == pt.SUBS else numberOfCentralVoxelsClassified[2]
#=========================================================================================================================================
#Grab the central voxels of the predicted fms from the cnn in this batch.
centralVoxelsOfAllFmsInLayer = fmsReturnedForATestBatchForCertainLayer[:, #batchsize
:, #number of featuremaps
rOfTopLeftCentralVoxelAtTheFm:
rOfTopLeftCentralVoxelAtTheFm
+
numberOfCentralVoxelsToGetInDirectionR,
cOfTopLeftCentralVoxelAtTheFm:
cOfTopLeftCentralVoxelAtTheFm
+
numberOfCentralVoxelsToGetInDirectionC,
zOfTopLeftCentralVoxelAtTheFm:
zOfTopLeftCentralVoxelAtTheFm
+
numberOfCentralVoxelsToGetInDirectionZ]
#If the pathway that is visualised currently is the subsampled, I need to upsample the central voxels to the normal resolution, before reconstructing the image-fm.
if pathway.pType(
) == pt.SUBS: #subsampled layer. Remember that this returns smaller dimension outputs, cause it works in the subsampled space. I need to repeat it, to bring it to the dimensions of the normal-voxel-space.
expandedOutputOfFmsR = np.repeat(
centralVoxelsOfAllFmsInLayer,
pathway.subsFactor()[0],
axis=2)
expandedOutputOfFmsRC = np.repeat(
expandedOutputOfFmsR,
pathway.subsFactor()[1],
axis=3)
expandedOutputOfFmsRCZ = np.repeat(
expandedOutputOfFmsRC,
pathway.subsFactor()[2],
axis=4)
#The below is a trick to get correct number of voxels even when subsampling factor is even or not exact divisor of the number of central voxels.
#...This trick is coupled with the ceil() when getting the numberOfCentralVoxelsToGetInDirectionR above.
centralVoxelsOfAllFmsToBeVisualisedForWholeBatch = expandedOutputOfFmsRCZ[:, :, 0:numberOfCentralVoxelsClassified[
0], 0:numberOfCentralVoxelsClassified[
1], 0:numberOfCentralVoxelsClassified[2]]
else:
centralVoxelsOfAllFmsToBeVisualisedForWholeBatch = centralVoxelsOfAllFmsInLayer
#----For every image part within this batch, reconstruct the corresponding part of the feature maps of the layer we are currently visualising in this loop.
for imagePart_in_this_batch_i in range(batchsize):
#Now put the label-cube in the new-label-segmentation-image, at the correct position.
#The very first label goes not in index 0,0,0 but half-patch further away! At the position of the central voxel of the top-left patch!
sliceCoordsOfThisSegment = sliceCoordsOfSegmentsInImage[
imagePartOfConstructedFeatureMaps_i +
imagePart_in_this_batch_i]
coordsOfTopLeftVoxelForThisPart = [
sliceCoordsOfThisSegment[0][0],
sliceCoordsOfThisSegment[1][0],
sliceCoordsOfThisSegment[2][0]
]
fmImageInMultidimArrayToReconstructInThisIteration[ # I put the central-predicted-voxels of all FMs to the corresponding, newly created images all at once.
:, #last dimension is the number-of-Fms, I create an image for each.
coordsOfTopLeftVoxelForThisPart[0] +
rczHalfRecFieldCnn[0]:
coordsOfTopLeftVoxelForThisPart[0] +
rczHalfRecFieldCnn[0] +
strideOfImagePartsPerDimensionInVoxels[0],
coordsOfTopLeftVoxelForThisPart[1] +
rczHalfRecFieldCnn[1]:
coordsOfTopLeftVoxelForThisPart[1] +
rczHalfRecFieldCnn[1] +
strideOfImagePartsPerDimensionInVoxels[1],
coordsOfTopLeftVoxelForThisPart[2] +
rczHalfRecFieldCnn[2]:
coordsOfTopLeftVoxelForThisPart[2] +
rczHalfRecFieldCnn[2] +
strideOfImagePartsPerDimensionInVoxels[
2]] = centralVoxelsOfAllFmsToBeVisualisedForWholeBatch[
imagePart_in_this_batch_i]
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray = highIndexOfFmsInTheMultidimensionalImageToFillInThisIterationExcluding
indexOfTheLayerInTheReturnedListByTheBatchTraining += 1
imagePartOfConstructedFeatureMaps_i += batchsize #all the image parts before this were reconstructed for all layers and feature maps. Next batch-iteration should start from this
#~~~~~~~~~~~~~~~~~~FINISHED CONSTRUCTING THE FEATURE MAPS FOR VISUALISATION~~~~~~~~~~
log.print3("TIMING: Segmentation of subject: [Extracting:] {0:.2f}".format(extractTimePerSubject) +\
" [Loading:] {0:.2f}".format(loadingTimePerSubject) +\
" [ForwardPass:] {0:.2f}".format(fwdPassTimePerSubject) +\
" [Total:] {0:.2f}".format(extractTimePerSubject+loadingTimePerSubject+fwdPassTimePerSubject) + " secs.")
# ================ SAVE PREDICTIONS =====================
#== saving predicted segmentations ==
predSegmentation = np.argmax(predProbMapsPerClass,
axis=0) #The segmentation.
unpaddedPredSegmentation = predSegmentation if not padInputImagesBool else unpadCnnOutputs(
predSegmentation, tupleOfPaddingPerAxesLeftRight)
# Multiply with the below to zero-out anything outside the RoiMask if given. Provided that RoiMask is binary [0,1].
unpaddedRoiMaskIfGivenElse1 = 1
if isinstance(roiMask, (np.ndarray)): #If roiMask was given:
unpaddedRoiMaskIfGivenElse1 = roiMask if not padInputImagesBool else unpadCnnOutputs(
roiMask, tupleOfPaddingPerAxesLeftRight)
if savePredictedSegmAndProbsDict[
"segm"] == True: #save predicted segmentation
suffixToAdd = suffixForSegmAndProbsDict["segm"]
#Save the image. Pass the filename paths of the normal image so that I can dublicate the header info, eg RAS transformation.
unpaddedPredSegmentationWithinRoi = unpaddedPredSegmentation * unpaddedRoiMaskIfGivenElse1
savePredImgToNiiWithOriginalHdr(
unpaddedPredSegmentationWithinRoi, namesForSavingSegmAndProbs,
listOfFilepathsToEachChannelOfEachPatient, image_i,
suffixToAdd, np.dtype(np.int16), log)
#== saving probability maps ==
for class_i in range(0, NUMBER_OF_CLASSES):
if (len(savePredictedSegmAndProbsDict["prob"]) >= class_i +
1) and (savePredictedSegmAndProbsDict["prob"][class_i]
== True): #save predicted probMap for class
suffixToAdd = suffixForSegmAndProbsDict["prob"] + str(class_i)
#Save the image. Pass the filename paths of the normal image so that I can dublicate the header info, eg RAS transformation.
predProbMapClassI = predProbMapsPerClass[class_i, :, :, :]
unpaddedPredProbMapClassI = predProbMapClassI if not padInputImagesBool else unpadCnnOutputs(
predProbMapClassI, tupleOfPaddingPerAxesLeftRight)
unpaddedPredProbMapClassIWithinRoi = unpaddedPredProbMapClassI * unpaddedRoiMaskIfGivenElse1
savePredImgToNiiWithOriginalHdr(
unpaddedPredProbMapClassIWithinRoi,
namesForSavingSegmAndProbs,
listOfFilepathsToEachChannelOfEachPatient, image_i,
suffixToAdd, np.dtype(np.float32), log)
#== saving feature maps ==
if saveIndividualFmImagesForVisualisation:
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray = 0
for pathway_i in range(len(cnn3d.pathways)):
pathway = cnn3d.pathways[pathway_i]
indicesOfFmsToVisualisePerLayerOfCertainPathway = indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[
pathway.pType()]
if indicesOfFmsToVisualisePerLayerOfCertainPathway != []:
for layer_i in range(len(pathway.getLayers())):
indicesOfFmsToVisualiseForCertainLayerOfCertainPathway = indicesOfFmsToVisualisePerLayerOfCertainPathway[
layer_i]
if indicesOfFmsToVisualiseForCertainLayerOfCertainPathway!=[] :
#If the user specifies to grab more feature maps than exist (eg 9999), correct it, replacing it with the number of FMs in the layer.
for fmActualNumber in range(
indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[
0],
indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[
1]):
fmToSave = multidimensionalImageWithAllToBeVisualisedFmsArray[
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray]
unpaddedFmToSave = fmToSave if not padInputImagesBool else unpadCnnOutputs(
fmToSave, tupleOfPaddingPerAxesLeftRight)
saveFmImgToNiiWithOriginalHdr(
unpaddedFmToSave, namesForSavingFms,
listOfFilepathsToEachChannelOfEachPatient,
image_i, pathway_i, layer_i,
fmActualNumber, log)
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray += 1
if saveMultidimensionalImageWithAllFms:
multidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms = np.transpose(
multidimensionalImageWithAllToBeVisualisedFmsArray,
(1, 2, 3, 0))
unpaddedMultidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms = multidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms if not padInputImagesBool else \
unpadCnnOutputs(multidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms, tupleOfPaddingPerAxesLeftRight)
#Save a multidimensional Nii image. 3D Image, with the 4th dimension being all the Fms...
save4DImgWithAllFmsToNiiWithOriginalHdr(
unpaddedMultidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms,
namesForSavingFms, listOfFilepathsToEachChannelOfEachPatient,
image_i, log)
#================= FINISHED SAVING RESULTS ====================
#================= EVALUATE DSC FOR EACH SUBJECT ========================
if providedGtLabelsBool: # Ground Truth was provided for calculation of DSC. Do DSC calculation.
log.print3(
"+++++++++++++++++++++ Reporting Segmentation Metrics for the subject #"
+ str(image_i) + " ++++++++++++++++++++++++++")
#Unpad whatever needed.
unpaddedGtLabelsImage = gtLabelsImage if not padInputImagesBool else unpadCnnOutputs(
gtLabelsImage, tupleOfPaddingPerAxesLeftRight)
#calculate DSC per class.
for class_i in range(0, NUMBER_OF_CLASSES):
if class_i == 0: #in this case, do the evaluation for the segmentation of the WHOLE FOREGROUND (ie, all classes merged except background)
binaryPredSegmClassI = unpaddedPredSegmentation > 0 # Merge every class except the background (assumed to be label == 0 )
binaryGtLabelClassI = unpaddedGtLabelsImage > 0
else:
binaryPredSegmClassI = unpaddedPredSegmentation == class_i
binaryGtLabelClassI = unpaddedGtLabelsImage == class_i
binaryPredSegmClassIWithinRoi = binaryPredSegmClassI * unpaddedRoiMaskIfGivenElse1
#Calculate the 3 Dices. Dice1 = Allpredicted/allLesions, Dice2 = PredictedWithinRoiMask / AllLesions , Dice3 = PredictedWithinRoiMask / LesionsInsideRoiMask.
#Dice1 = Allpredicted/allLesions
diceCoeff1 = calculateDiceCoefficient(binaryPredSegmClassI,
binaryGtLabelClassI)
diceCoeffs1[image_i][
class_i] = diceCoeff1 if diceCoeff1 != -1 else NA_PATTERN
#Dice2 = PredictedWithinRoiMask / AllLesions
diceCoeff2 = calculateDiceCoefficient(
binaryPredSegmClassIWithinRoi, binaryGtLabelClassI)
diceCoeffs2[image_i][
class_i] = diceCoeff2 if diceCoeff2 != -1 else NA_PATTERN
#Dice3 = PredictedWithinRoiMask / LesionsInsideRoiMask
diceCoeff3 = calculateDiceCoefficient(
binaryPredSegmClassIWithinRoi,
binaryGtLabelClassI * unpaddedRoiMaskIfGivenElse1)
diceCoeffs3[image_i][
class_i] = diceCoeff3 if diceCoeff3 != -1 else NA_PATTERN
log.print3(
"ACCURACY: (" + str(validation_or_testing_str) +
") The Per-Class DICE Coefficients for subject with index #" +
str(image_i) + " equal: DICE1=" +
strListFl4fNA(diceCoeffs1[image_i], NA_PATTERN) + " DICE2=" +
strListFl4fNA(diceCoeffs2[image_i], NA_PATTERN) + " DICE3=" +
strListFl4fNA(diceCoeffs3[image_i], NA_PATTERN))
printExplanationsAboutDice(log)
#================= Loops for all patients have finished. Now lets just report the average DSC over all the processed patients. ====================
if providedGtLabelsBool and total_number_of_images > 0: # Ground Truth was provided for calculation of DSC. Do DSC calculation.
log.print3(
"+++++++++++++++++++++++++++++++ Segmentation of all subjects finished +++++++++++++++++++++++++++++++++++"
)
log.print3(
"+++++++++++++++++++++ Reporting Average Segmentation Metrics over all subjects ++++++++++++++++++++++++++"
)
meanDiceCoeffs1 = getMeanPerColOf2dListExclNA(diceCoeffs1, NA_PATTERN)
meanDiceCoeffs2 = getMeanPerColOf2dListExclNA(diceCoeffs2, NA_PATTERN)
meanDiceCoeffs3 = getMeanPerColOf2dListExclNA(diceCoeffs3, NA_PATTERN)
log.print3(
"ACCURACY: (" + str(validation_or_testing_str) +
") The Per-Class average DICE Coefficients over all subjects are: DICE1="
+ strListFl4fNA(meanDiceCoeffs1, NA_PATTERN) + " DICE2=" +
strListFl4fNA(meanDiceCoeffs2, NA_PATTERN) + " DICE3=" +
strListFl4fNA(meanDiceCoeffs3, NA_PATTERN))
printExplanationsAboutDice(log)
end_time = time.time()
log.print3("TIMING: " + validation_or_testing_str +
" process lasted: {0:.2f}".format(end_time - start_time) +
" secs.")
log.print3(
"###########################################################################################################"
)
log.print3("############################# Finished full Segmentation of " +
str(validation_or_testing_str) +
" subjects ##########################")
log.print3(
"###########################################################################################################"
)
return 0
def inferenceWholeVolumes( sessionTf,
cnn3d,
log,
val_or_test,
savePredictedSegmAndProbsDict,
listOfFilepathsToEachChannelOfEachPatient,
providedGtLabelsBool, #boolean. DSC calculation will be performed if this is provided.
listOfFilepathsToGtLabelsOfEachPatient,
providedRoiMaskForFastInfBool,
listOfFilepathsToRoiMaskFastInfOfEachPatient,
namesForSavingSegmAndProbs,
suffixForSegmAndProbsDict,
# Hyper parameters
batchsize,
#----Preprocessing------
padInputImagesBool,
#--------For FM visualisation---------
saveIndividualFmImagesForVisualisation,
saveMultidimensionalImageWithAllFms,
indicesOfFmsToVisualisePerPathwayTypeAndPerLayer,
namesForSavingFms ) :
# saveIndividualFmImagesForVisualisation: should contain an entry per pathwayType, even if just []...
# ... If not [], the list should contain one entry per layer of the pathway, even if just [].
# ... The layer entries, if not [], they should have to integers, lower and upper FM to visualise. Excluding the highest index.
validation_or_testing_str = "Validation" if val_or_test == "val" else "Testing"
log.print3("###########################################################################################################")
log.print3("############################# Starting full Segmentation of " + str(validation_or_testing_str) + " subjects ##########################")
log.print3("###########################################################################################################")
start_time = time.time()
NA_PATTERN = AccuracyOfEpochMonitorSegmentation.NA_PATTERN
NUMBER_OF_CLASSES = cnn3d.num_classes
total_number_of_images = len(listOfFilepathsToEachChannelOfEachPatient)
#one dice score for whole + for each class)
# A list of dimensions: total_number_of_images X NUMBER_OF_CLASSES
diceCoeffs1 = [ [-1] * NUMBER_OF_CLASSES for i in range(total_number_of_images) ] #AllpredictedLes/AllLesions
diceCoeffs2 = [ [-1] * NUMBER_OF_CLASSES for i in range(total_number_of_images) ] #predictedInsideRoiMask/AllLesions
diceCoeffs3 = [ [-1] * NUMBER_OF_CLASSES for i in range(total_number_of_images) ] #predictedInsideRoiMask/ LesionsInsideRoiMask (for comparisons)
recFieldCnn = cnn3d.recFieldCnn
#stride is how much I move in each dimension to acquire the next imagePart.
#I move exactly the number I segment in the centre of each image part (originally this was 9^3 segmented per imagePart).
numberOfCentralVoxelsClassified = cnn3d.finalTargetLayer.outputShape["test"][2:]
strideOfImagePartsPerDimensionInVoxels = numberOfCentralVoxelsClassified
rczHalfRecFieldCnn = [ (recFieldCnn[i]-1)//2 for i in range(3) ]
#Find the total number of feature maps that will be created:
#NOTE: saveIndividualFmImagesForVisualisation should contain an entry per pathwayType, even if just []. If not [], the list should contain one entry per layer of the pathway, even if just []. The layer entries, if not [], they should have to integers, lower and upper FM to visualise.
if saveIndividualFmImagesForVisualisation or saveMultidimensionalImageWithAllFms:
totalNumberOfFMsToProcess = 0
for pathway in cnn3d.pathways :
indicesOfFmsToVisualisePerLayerOfCertainPathway = indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[ pathway.pType() ]
if indicesOfFmsToVisualisePerLayerOfCertainPathway != [] :
for layer_i in range(len(pathway.getLayers())) :
indicesOfFmsToVisualiseForCertainLayerOfCertainPathway = indicesOfFmsToVisualisePerLayerOfCertainPathway[layer_i]
if indicesOfFmsToVisualiseForCertainLayerOfCertainPathway!=[] :
#If the user specifies to grab more feature maps than exist (eg 9999), correct it, replacing it with the number of FMs in the layer.
numberOfFeatureMapsInThisLayer = pathway.getLayer(layer_i).getNumberOfFeatureMaps()
indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[1] = min(indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[1], numberOfFeatureMapsInThisLayer)
totalNumberOfFMsToProcess += indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[1] - indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[0]
for image_i in range(total_number_of_images) :
log.print3("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
log.print3("~~~~~~~~~~~~~~~~~~~~ Segmenting subject with index #"+str(image_i)+" ~~~~~~~~~~~~~~~~~~~~")
#load the image channels in cpu
[imageChannels,
gtLabelsImage, #only for accurate/correct DICE1-2 calculation
roiMask,
arrayWithWeightMapsWhereToSampleForEachCategory, #only used in training. Placeholder here.
tupleOfPaddingPerAxesLeftRight #( (padLeftR, padRightR), (padLeftC,padRightC), (padLeftZ,padRightZ)). All 0s when no padding.
] = load_imgs_of_subject(
log,
None,
"test",
False, # run_input_checks.
image_i,
listOfFilepathsToEachChannelOfEachPatient,
providedGtLabelsBool,
listOfFilepathsToGtLabelsOfEachPatient,
cnn3d.num_classes,
False, # providedWeightMapsToSampleForEachCategory
None,
providedRoiMaskForFastInfBool,
listOfFilepathsToRoiMaskFastInfOfEachPatient,
padInputImagesBool,
recFieldCnn, # only used if padInputsBool
cnn3d.pathways[0].getShapeOfInput("test")[2:] # dimsOfPrimeSegmentRcz, for padding
)
niiDimensions = list(imageChannels.shape[1:])
#The predicted probability-maps for the whole volume, one per class. Will be constructed by stitching together the predictions from each segment.
predProbMapsPerClass = np.zeros([NUMBER_OF_CLASSES]+niiDimensions, dtype = "float32")
#create the big array that will hold all the fms (for feature extraction, to save as a big multi-dim image).
if saveIndividualFmImagesForVisualisation or saveMultidimensionalImageWithAllFms:
multidimensionalImageWithAllToBeVisualisedFmsArray = np.zeros([totalNumberOfFMsToProcess] + niiDimensions, dtype = "float32")
# Tile the image and get all slices of the segments that it fully breaks down to.
[sliceCoordsOfSegmentsInImage] = getCoordsOfAllSegmentsOfAnImage(log,
cnn3d.pathways[0].getShapeOfInput("test")[2:], # dimsOfPrimarySegment
strideOfImagePartsPerDimensionInVoxels,
batchsize,
imageChannels,
roiMask )
log.print3("Starting to segment each image-part by calling the cnn.cnnTestModel(i). This part takes a few mins per volume...")
num_segments_for_case = len(sliceCoordsOfSegmentsInImage)
log.print3("Total number of Segments to process:"+str(num_segments_for_case))
imagePartOfConstructedProbMap_i = 0
imagePartOfConstructedFeatureMaps_i = 0
num_batches = num_segments_for_case//batchsize
extractTimePerSubject = 0; loadingTimePerSubject = 0; fwdPassTimePerSubject = 0
for batch_i in range(num_batches) :
print_progress_step = max(1, num_batches//5)
if batch_i == 0 or ((batch_i+1) % print_progress_step) == 0 or (batch_i+1) == num_batches :
log.print3("Processed "+str((batch_i+1)*batchsize)+"/"+str(num_segments_for_case)+" segments.")
# Extract the data for the segments of this batch. ( I could modularize extractDataOfASegmentFromImagesUsingSampledSliceCoords() of training and use it here as well. )
start_extract_time = time.time()
sliceCoordsOfSegmentsInBatch = sliceCoordsOfSegmentsInImage[ batch_i*batchsize : (batch_i+1)*batchsize ]
[channsOfSegmentsPerPath] = extractSegmentsGivenSliceCoords(cnn3d,
sliceCoordsOfSegmentsInBatch,
imageChannels,
recFieldCnn )
end_extract_time = time.time()
extractTimePerSubject += end_extract_time - start_extract_time
# ======= Run the inference ============
ops_to_fetch = cnn3d.get_main_ops('test')
list_of_ops = [ ops_to_fetch['pred_probs'] ] + ops_to_fetch['list_of_fms_per_layer']
# No loading of data in bulk as in training, cause here it's only 1 batch per iteration.
start_loading_time = time.time()
feeds = cnn3d.get_main_feeds('test')
feeds_dict = { feeds['x'] : np.asarray(channsOfSegmentsPerPath[0], dtype='float32') }
for path_i in range(len(channsOfSegmentsPerPath[1:])) :
feeds_dict.update( { feeds['x_sub_'+str(path_i)]: np.asarray(channsOfSegmentsPerPath[1+path_i], dtype='float32') } )
end_loading_time = time.time()
loadingTimePerSubject += end_loading_time - start_loading_time
start_testing_time = time.time()
# Forward pass
# featureMapsOfEachLayerAndPredictionProbabilitiesAtEndForATestBatch = cnn3d.cnnTestAndVisualiseAllFmsFunction( *input_args_to_net )
featureMapsOfEachLayerAndPredictionProbabilitiesAtEndForATestBatch = sessionTf.run( fetches=list_of_ops, feed_dict=feeds_dict )
end_testing_time = time.time()
fwdPassTimePerSubject += end_testing_time - start_testing_time
predictionForATestBatch = featureMapsOfEachLayerAndPredictionProbabilitiesAtEndForATestBatch[0]
listWithTheFmsOfAllLayersSortedByPathwayTypeForTheBatch = featureMapsOfEachLayerAndPredictionProbabilitiesAtEndForATestBatch[1:] # If no FMs visualised, this should return []
#No reshape needed, cause I now do it internally. But to dimensions (batchSize, FMs, R,C,Z).
#~~~~~~~~~~~~~~~~CONSTRUCT THE PREDICTED PROBABILITY MAPS~~~~~~~~~~~~~~
#From the results of this batch, create the prediction image by putting the predictions to the correct place in the image.
for imagePart_in_this_batch_i in range(batchsize) :
#Now put the label-cube in the new-label-segmentation-image, at the correct position.
#The very first label goes not in index 0,0,0 but half-patch further away! At the position of the central voxel of the top-left patch!
sliceCoordsOfThisSegment = sliceCoordsOfSegmentsInImage[imagePartOfConstructedProbMap_i]
coordsOfTopLeftVoxelForThisPart = [ sliceCoordsOfThisSegment[0][0], sliceCoordsOfThisSegment[1][0], sliceCoordsOfThisSegment[2][0] ]
predProbMapsPerClass[
:,
coordsOfTopLeftVoxelForThisPart[0] + rczHalfRecFieldCnn[0] : coordsOfTopLeftVoxelForThisPart[0] + rczHalfRecFieldCnn[0] + strideOfImagePartsPerDimensionInVoxels[0],
coordsOfTopLeftVoxelForThisPart[1] + rczHalfRecFieldCnn[1] : coordsOfTopLeftVoxelForThisPart[1] + rczHalfRecFieldCnn[1] + strideOfImagePartsPerDimensionInVoxels[1],
coordsOfTopLeftVoxelForThisPart[2] + rczHalfRecFieldCnn[2] : coordsOfTopLeftVoxelForThisPart[2] + rczHalfRecFieldCnn[2] + strideOfImagePartsPerDimensionInVoxels[2],
] = predictionForATestBatch[imagePart_in_this_batch_i]
imagePartOfConstructedProbMap_i += 1
#~~~~~~~~~~~~~FINISHED CONSTRUCTING THE PREDICTED PROBABILITY MAPS~~~~~~~
#~~~~~~~~~~~~~~CONSTRUCT THE FEATURE MAPS FOR VISUALISATION~~~~~~~~~~~~~~~~~
if saveIndividualFmImagesForVisualisation or saveMultidimensionalImageWithAllFms:
fmsReturnedForATestBatchForCertainLayer = None
#currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray is the index in the multidimensional array that holds all the to-be-visualised-fms. It is the one that corresponds to the next to-be-visualised indexOfTheLayerInTheReturnedListByTheBatchTraining.
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray = 0
#indexOfTheLayerInTheReturnedListByTheBatchTraining is the index over all the layers in the returned list. I will work only with the ones specified to visualise.
indexOfTheLayerInTheReturnedListByTheBatchTraining = 0
for pathway in cnn3d.pathways :
for layer_i in range(len(pathway.getLayers())) :
if indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[ pathway.pType() ]==[] or indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[ pathway.pType() ][layer_i]==[] :
continue
indicesOfFmsToExtractFromThisLayer = indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[ pathway.pType() ][layer_i]
fmsReturnedForATestBatchForCertainLayer = listWithTheFmsOfAllLayersSortedByPathwayTypeForTheBatch[indexOfTheLayerInTheReturnedListByTheBatchTraining]
#We specify a range of fms to visualise from a layer. currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray : highIndexOfFmsInTheMultidimensionalImageToFillInThisIterationExcluding defines were to put them in the multidimensional-image-array.
highIndexOfFmsInTheMultidimensionalImageToFillInThisIterationExcluding = currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray + indicesOfFmsToExtractFromThisLayer[1] - indicesOfFmsToExtractFromThisLayer[0]
fmImageInMultidimArrayToReconstructInThisIteration = multidimensionalImageWithAllToBeVisualisedFmsArray[currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray: highIndexOfFmsInTheMultidimensionalImageToFillInThisIterationExcluding]
#=========================================================================================================================================
#====the following calculations could be move OUTSIDE THE FOR LOOPS, by using the kernel-size parameter (from the cnn instance) instead of the shape of the returned value.
#====fmsReturnedForATestBatchForCertainLayer.shape[2] - (numberOfCentralVoxelsClassified[0]-1) is essentially the width of the patch left after the convolutions.
#====These calculations are pathway and layer-specific. So they could be done once, prior to image processing, and results cached in a list to be accessed during the loop.
numberOfVoxToSubtrToGetPatchWidthAtThisFm_R = numberOfCentralVoxelsClassified[0]-1 if pathway.pType() != pt.SUBS else int(math.ceil((numberOfCentralVoxelsClassified[0]*1.0)/pathway.subsFactor()[0]) -1)
numberOfVoxToSubtrToGetPatchWidthAtThisFm_C = numberOfCentralVoxelsClassified[1]-1 if pathway.pType() != pt.SUBS else int(math.ceil((numberOfCentralVoxelsClassified[1]*1.0)/pathway.subsFactor()[1]) -1)
numberOfVoxToSubtrToGetPatchWidthAtThisFm_Z = numberOfCentralVoxelsClassified[2]-1 if pathway.pType() != pt.SUBS else int(math.ceil((numberOfCentralVoxelsClassified[2]*1.0)/pathway.subsFactor()[2]) -1)
rPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions = fmsReturnedForATestBatchForCertainLayer.shape[2] - numberOfVoxToSubtrToGetPatchWidthAtThisFm_R
cPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions = fmsReturnedForATestBatchForCertainLayer.shape[3] - numberOfVoxToSubtrToGetPatchWidthAtThisFm_C
zPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions = fmsReturnedForATestBatchForCertainLayer.shape[4] - numberOfVoxToSubtrToGetPatchWidthAtThisFm_Z
rOfTopLeftCentralVoxelAtTheFm = (rPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions-1)//2 #-1 so that if width is even, I'll get the left voxel from the centre as 1st, which I THINK is how I am getting the patches from the original image.
cOfTopLeftCentralVoxelAtTheFm = (cPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions-1)//2
zOfTopLeftCentralVoxelAtTheFm = (zPatchDimensionAtTheFmThatWeVisualiseAfterConvolutions-1)//2
#the math.ceil / subsamplingFactor is a trick to make it work for even subsamplingFactor too. Eg 9/2=4.5 => Get 5. Combined with the trick at repeat, I get my correct number of central voxels hopefully.
numberOfCentralVoxelsToGetInDirectionR = int(math.ceil((numberOfCentralVoxelsClassified[0]*1.0)/pathway.subsFactor()[0])) if pathway.pType() == pt.SUBS else numberOfCentralVoxelsClassified[0]
numberOfCentralVoxelsToGetInDirectionC = int(math.ceil((numberOfCentralVoxelsClassified[1]*1.0)/pathway.subsFactor()[1])) if pathway.pType() == pt.SUBS else numberOfCentralVoxelsClassified[1]
numberOfCentralVoxelsToGetInDirectionZ = int(math.ceil((numberOfCentralVoxelsClassified[2]*1.0)/pathway.subsFactor()[2])) if pathway.pType() == pt.SUBS else numberOfCentralVoxelsClassified[2]
#=========================================================================================================================================
#Grab the central voxels of the predicted fms from the cnn in this batch.
centralVoxelsOfAllFmsInLayer = fmsReturnedForATestBatchForCertainLayer[:, #batchsize
:, #number of featuremaps
rOfTopLeftCentralVoxelAtTheFm:rOfTopLeftCentralVoxelAtTheFm+numberOfCentralVoxelsToGetInDirectionR,
cOfTopLeftCentralVoxelAtTheFm:cOfTopLeftCentralVoxelAtTheFm+numberOfCentralVoxelsToGetInDirectionC,
zOfTopLeftCentralVoxelAtTheFm:zOfTopLeftCentralVoxelAtTheFm+numberOfCentralVoxelsToGetInDirectionZ
]
#If the pathway that is visualised currently is the subsampled, I need to upsample the central voxels to the normal resolution, before reconstructing the image-fm.
if pathway.pType() == pt.SUBS : #subsampled layer. Remember that this returns smaller dimension outputs, cause it works in the subsampled space. I need to repeat it, to bring it to the dimensions of the normal-voxel-space.
expandedOutputOfFmsR = np.repeat(centralVoxelsOfAllFmsInLayer, pathway.subsFactor()[0],axis = 2)
expandedOutputOfFmsRC = np.repeat(expandedOutputOfFmsR, pathway.subsFactor()[1],axis = 3)
expandedOutputOfFmsRCZ = np.repeat(expandedOutputOfFmsRC, pathway.subsFactor()[2],axis = 4)
#The below is a trick to get correct number of voxels even when subsampling factor is even or not exact divisor of the number of central voxels.
#...This trick is coupled with the ceil() when getting the numberOfCentralVoxelsToGetInDirectionR above.
centralVoxelsOfAllFmsToBeVisualisedForWholeBatch = expandedOutputOfFmsRCZ[:,
:,
0:numberOfCentralVoxelsClassified[0],
0:numberOfCentralVoxelsClassified[1],
0:numberOfCentralVoxelsClassified[2]
]
else :
centralVoxelsOfAllFmsToBeVisualisedForWholeBatch = centralVoxelsOfAllFmsInLayer
#----For every image part within this batch, reconstruct the corresponding part of the feature maps of the layer we are currently visualising in this loop.
for imagePart_in_this_batch_i in range(batchsize) :
#Now put the label-cube in the new-label-segmentation-image, at the correct position.
#The very first label goes not in index 0,0,0 but half-patch further away! At the position of the central voxel of the top-left patch!
sliceCoordsOfThisSegment = sliceCoordsOfSegmentsInImage[imagePartOfConstructedFeatureMaps_i + imagePart_in_this_batch_i]
coordsOfTopLeftVoxelForThisPart = [ sliceCoordsOfThisSegment[0][0], sliceCoordsOfThisSegment[1][0], sliceCoordsOfThisSegment[2][0] ]
fmImageInMultidimArrayToReconstructInThisIteration[ # I put the central-predicted-voxels of all FMs to the corresponding, newly created images all at once.
:, #last dimension is the number-of-Fms, I create an image for each.
coordsOfTopLeftVoxelForThisPart[0] + rczHalfRecFieldCnn[0] : coordsOfTopLeftVoxelForThisPart[0] + rczHalfRecFieldCnn[0] + strideOfImagePartsPerDimensionInVoxels[0],
coordsOfTopLeftVoxelForThisPart[1] + rczHalfRecFieldCnn[1] : coordsOfTopLeftVoxelForThisPart[1] + rczHalfRecFieldCnn[1] + strideOfImagePartsPerDimensionInVoxels[1],
coordsOfTopLeftVoxelForThisPart[2] + rczHalfRecFieldCnn[2] : coordsOfTopLeftVoxelForThisPart[2] + rczHalfRecFieldCnn[2] + strideOfImagePartsPerDimensionInVoxels[2]
] = centralVoxelsOfAllFmsToBeVisualisedForWholeBatch[imagePart_in_this_batch_i]
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray = highIndexOfFmsInTheMultidimensionalImageToFillInThisIterationExcluding
indexOfTheLayerInTheReturnedListByTheBatchTraining += 1
imagePartOfConstructedFeatureMaps_i += batchsize #all the image parts before this were reconstructed for all layers and feature maps. Next batch-iteration should start from this
#~~~~~~~~~~~~~~~~~~FINISHED CONSTRUCTING THE FEATURE MAPS FOR VISUALISATION~~~~~~~~~~
log.print3("TIMING: Segmentation of subject: [Extracting:] {0:.2f}".format(extractTimePerSubject) +\
" [Loading:] {0:.2f}".format(loadingTimePerSubject) +\
" [ForwardPass:] {0:.2f}".format(fwdPassTimePerSubject) +\
" [Total:] {0:.2f}".format(extractTimePerSubject+loadingTimePerSubject+fwdPassTimePerSubject) + " secs.")
# ================ SAVE PREDICTIONS =====================
#== saving predicted segmentations ==
predSegmentation = np.argmax(predProbMapsPerClass, axis=0) #The segmentation.
unpaddedPredSegmentation = predSegmentation if not padInputImagesBool else unpadCnnOutputs(predSegmentation, tupleOfPaddingPerAxesLeftRight)
# Multiply with the below to zero-out anything outside the RoiMask if given. Provided that RoiMask is binary [0,1].
unpaddedRoiMaskIfGivenElse1 = 1
if isinstance(roiMask, (np.ndarray)) : #If roiMask was given:
unpaddedRoiMaskIfGivenElse1 = roiMask if not padInputImagesBool else unpadCnnOutputs(roiMask, tupleOfPaddingPerAxesLeftRight)
if savePredictedSegmAndProbsDict["segm"] == True : #save predicted segmentation
suffixToAdd = suffixForSegmAndProbsDict["segm"]
#Save the image. Pass the filename paths of the normal image so that I can dublicate the header info, eg RAS transformation.
unpaddedPredSegmentationWithinRoi = unpaddedPredSegmentation * unpaddedRoiMaskIfGivenElse1
savePredImgToNiiWithOriginalHdr( unpaddedPredSegmentationWithinRoi,
namesForSavingSegmAndProbs,
listOfFilepathsToEachChannelOfEachPatient,
image_i,
suffixToAdd,
np.dtype(np.int16),
log )
#== saving probability maps ==
for class_i in range(0, NUMBER_OF_CLASSES) :
if (len(savePredictedSegmAndProbsDict["prob"]) >= class_i + 1) and (savePredictedSegmAndProbsDict["prob"][class_i] == True) : #save predicted probMap for class
suffixToAdd = suffixForSegmAndProbsDict["prob"] + str(class_i)
#Save the image. Pass the filename paths of the normal image so that I can dublicate the header info, eg RAS transformation.
predProbMapClassI = predProbMapsPerClass[class_i,:,:,:]
unpaddedPredProbMapClassI = predProbMapClassI if not padInputImagesBool else unpadCnnOutputs(predProbMapClassI, tupleOfPaddingPerAxesLeftRight)
unpaddedPredProbMapClassIWithinRoi = unpaddedPredProbMapClassI * unpaddedRoiMaskIfGivenElse1
savePredImgToNiiWithOriginalHdr( unpaddedPredProbMapClassIWithinRoi,
namesForSavingSegmAndProbs,
listOfFilepathsToEachChannelOfEachPatient,
image_i,
suffixToAdd,
np.dtype(np.float32),
log )
#== saving feature maps ==
if saveIndividualFmImagesForVisualisation :
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray = 0
for pathway_i in range( len(cnn3d.pathways) ) :
pathway = cnn3d.pathways[pathway_i]
indicesOfFmsToVisualisePerLayerOfCertainPathway = indicesOfFmsToVisualisePerPathwayTypeAndPerLayer[ pathway.pType() ]
if indicesOfFmsToVisualisePerLayerOfCertainPathway!=[] :
for layer_i in range( len(pathway.getLayers()) ) :
indicesOfFmsToVisualiseForCertainLayerOfCertainPathway = indicesOfFmsToVisualisePerLayerOfCertainPathway[layer_i]
if indicesOfFmsToVisualiseForCertainLayerOfCertainPathway!=[] :
#If the user specifies to grab more feature maps than exist (eg 9999), correct it, replacing it with the number of FMs in the layer.
for fmActualNumber in range(indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[0], indicesOfFmsToVisualiseForCertainLayerOfCertainPathway[1]) :
fmToSave = multidimensionalImageWithAllToBeVisualisedFmsArray[currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray]
unpaddedFmToSave = fmToSave if not padInputImagesBool else unpadCnnOutputs(fmToSave, tupleOfPaddingPerAxesLeftRight)
saveFmImgToNiiWithOriginalHdr( unpaddedFmToSave,
namesForSavingFms,
listOfFilepathsToEachChannelOfEachPatient,
image_i,
pathway_i,
layer_i,
fmActualNumber,
log )
currentIndexInTheMultidimensionalImageWithAllToBeVisualisedFmsArray += 1
if saveMultidimensionalImageWithAllFms :
multidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms = np.transpose(multidimensionalImageWithAllToBeVisualisedFmsArray, (1,2,3, 0) )
unpaddedMultidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms = multidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms if not padInputImagesBool else \
unpadCnnOutputs(multidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms, tupleOfPaddingPerAxesLeftRight)
#Save a multidimensional Nii image. 3D Image, with the 4th dimension being all the Fms...
save4DImgWithAllFmsToNiiWithOriginalHdr( unpaddedMultidimensionalImageWithAllToBeVisualisedFmsArrayWith4thDimAsFms,
namesForSavingFms,
listOfFilepathsToEachChannelOfEachPatient,
image_i,
log )
#================= FINISHED SAVING RESULTS ====================
#================= EVALUATE DSC FOR EACH SUBJECT ========================
if providedGtLabelsBool : # Ground Truth was provided for calculation of DSC. Do DSC calculation.
log.print3("+++++++++++++++++++++ Reporting Segmentation Metrics for the subject #" + str(image_i) + " ++++++++++++++++++++++++++")
#Unpad whatever needed.
unpaddedGtLabelsImage = gtLabelsImage if not padInputImagesBool else unpadCnnOutputs(gtLabelsImage, tupleOfPaddingPerAxesLeftRight)
#calculate DSC per class.
for class_i in range(0, NUMBER_OF_CLASSES) :
if class_i == 0 : #in this case, do the evaluation for the segmentation of the WHOLE FOREGROUND (ie, all classes merged except background)
binaryPredSegmClassI = unpaddedPredSegmentation > 0 # Merge every class except the background (assumed to be label == 0 )
binaryGtLabelClassI = unpaddedGtLabelsImage > 0
else :
binaryPredSegmClassI = unpaddedPredSegmentation == class_i
binaryGtLabelClassI = unpaddedGtLabelsImage == class_i
binaryPredSegmClassIWithinRoi = binaryPredSegmClassI * unpaddedRoiMaskIfGivenElse1
#Calculate the 3 Dices. Dice1 = Allpredicted/allLesions, Dice2 = PredictedWithinRoiMask / AllLesions , Dice3 = PredictedWithinRoiMask / LesionsInsideRoiMask.
#Dice1 = Allpredicted/allLesions
diceCoeff1 = calculateDiceCoefficient(binaryPredSegmClassI, binaryGtLabelClassI)
diceCoeffs1[image_i][class_i] = diceCoeff1 if diceCoeff1 != -1 else NA_PATTERN
#Dice2 = PredictedWithinRoiMask / AllLesions
diceCoeff2 = calculateDiceCoefficient(binaryPredSegmClassIWithinRoi, binaryGtLabelClassI)
diceCoeffs2[image_i][class_i] = diceCoeff2 if diceCoeff2 != -1 else NA_PATTERN
#Dice3 = PredictedWithinRoiMask / LesionsInsideRoiMask
diceCoeff3 = calculateDiceCoefficient(binaryPredSegmClassIWithinRoi, binaryGtLabelClassI * unpaddedRoiMaskIfGivenElse1)
diceCoeffs3[image_i][class_i] = diceCoeff3 if diceCoeff3 != -1 else NA_PATTERN
log.print3("ACCURACY: (" + str(validation_or_testing_str) + ") The Per-Class DICE Coefficients for subject with index #"+str(image_i)+" equal: DICE1="+strListFl4fNA(diceCoeffs1[image_i],NA_PATTERN)+" DICE2="+strListFl4fNA(diceCoeffs2[image_i],NA_PATTERN)+" DICE3="+strListFl4fNA(diceCoeffs3[image_i],NA_PATTERN))
printExplanationsAboutDice(log)
#================= Loops for all patients have finished. Now lets just report the average DSC over all the processed patients. ====================
if providedGtLabelsBool and total_number_of_images>0 : # Ground Truth was provided for calculation of DSC. Do DSC calculation.
log.print3("+++++++++++++++++++++++++++++++ Segmentation of all subjects finished +++++++++++++++++++++++++++++++++++")
log.print3("+++++++++++++++++++++ Reporting Average Segmentation Metrics over all subjects ++++++++++++++++++++++++++")
meanDiceCoeffs1 = getMeanPerColOf2dListExclNA(diceCoeffs1, NA_PATTERN)
meanDiceCoeffs2 = getMeanPerColOf2dListExclNA(diceCoeffs2, NA_PATTERN)
meanDiceCoeffs3 = getMeanPerColOf2dListExclNA(diceCoeffs3, NA_PATTERN)
log.print3("ACCURACY: (" + str(validation_or_testing_str) + ") The Per-Class average DICE Coefficients over all subjects are: DICE1=" + strListFl4fNA(meanDiceCoeffs1, NA_PATTERN) + " DICE2="+strListFl4fNA(meanDiceCoeffs2, NA_PATTERN)+" DICE3="+strListFl4fNA(meanDiceCoeffs3, NA_PATTERN))
printExplanationsAboutDice(log)
end_time = time.time()
log.print3("TIMING: "+validation_or_testing_str+" process lasted: {0:.2f}".format(end_time-start_time)+" secs.")
log.print3("###########################################################################################################")
log.print3("############################# Finished full Segmentation of " + str(validation_or_testing_str) + " subjects ##########################")
log.print3("###########################################################################################################")
return 0