Module ctsimu.processing.pipeline

Classes

class Pipeline (inputFileStack=None, outputFileStack=None)

Perform given processing steps on input images, save as output.

Parameters

inputFileStack : ImageStack or str

A string or an ImageStack object that specifies the path of the input image file(s).

outputFileStack : ImageStack or str

A string or an ImageStack object that specifies the path of the output image file(s).

Expand source code

class Pipeline:
    """ Perform given processing steps on input images, save as output. """

    def __init__(self, inputFileStack=None, outputFileStack=None):
        """
        Parameters
        ----------
        inputFileStack : ctsimu.image.ImageStack or str
            A string or an `ctsimu.image.ImageStack` object that specifies
            the path of the input image file(s).

        outputFileStack : ctsimu.image.ImageStack or str
            A string or an `ctsimu.image.ImageStack` object that specifies
            the path of the output image file(s).
        """

        self.inputFileStack   = None
        self.outputFileStack  = None

        self.setInputFileStack(inputFileStack)
        self.setOutputFileStack(outputFileStack)

        self.processingSteps = []

    def setInputFileStack(self, inputFileStack):
        """Set the input file stack.

        Parameters
        ----------
        inputFileStack : ctsimu.image.ImageStack or str
            A string or an `ctsimu.image.ImageStack` object that specifies
            the path of the input image file(s).
        """
        self.inputFileStack = createImageStack(inputFileStack)

    def setOutputFileStack(self, outputFileStack):
        """Set the output file parameters.

        Parameters
        ----------
        outputFileStack : ctsimu.image.ImageStack or str
            A string or an `ctsimu.image.ImageStack` object that specifies
            the path of the output image file(s).
        """
        self.outputFileStack = createImageStack(outputFileStack)

    def addStep(self, step):
        """Add a processing step to the pipeline.

        Parameters
        ----------
        step : ctsimu.processing.step.Step
        """
        if isinstance(step, Step):
            step.setPipeline(self)
            self.processingSteps.append(step)
        else:
            raise Exception("Failed to add processing step. Not a valid type of processing step: {}".format(step))

    def step(self, i:int):
        """Return step at position `i` in the pipeline.

        Parameters
        ----------
        i : int
            Step index (starting at zero).
        """

        if i < len(self.processingSteps):
            return self.processingSteps[i]
        else:
            raise Exception("Processing Pipeline: Requested processing step id (#{i}) exceeds number of stored processing steps ({n}).".format(i=i, n=len(self.processingSteps)))

    def run(self, overwrite:bool=True):
        """Run the processing pipeline with its current configuration.

        Parameters
        ----------
        overwrite : bool
            Overwrite existing image files?

            Default value: `True`
        """
        if self.inputFileStack is not None:
            nImagesProcessed = 0
            nImagesSkipped   = 0

            # Build stack if it hasn't been built yet:
            if not self.inputFileStack.built:
                self.inputFileStack.buildStack()

            saveOutputFiles = False
            if isinstance(self.outputFileStack, ImageStack):
                saveOutputFiles = True

                # Set output parameters to input parameters if no others given:
                if self.outputFileStack.getFileDataType() is None:
                    self.outputFileStack.setFileDataType(self.inputFileStack.getFileDataType())

                if self.outputFileStack.getFileByteOrder() is None:
                    self.outputFileStack.setFileByteOrder(self.inputFileStack.getFileByteOrder())

            # Treat projection files
            if self.inputFileStack.nSlices > 0:
                outputFiles = None               

                if saveOutputFiles:
                    outputFiles = self.outputFileStack.files
                    generalOutputName = self.outputFileStack.getFilename()
                    outputFolder   = os.path.dirname(generalOutputName)
                    outputBasename = os.path.basename(generalOutputName)

                    if outputFolder == "" or outputFolder is None:
                        outputFolder = "."

                    if '%' in outputBasename:
                        self.outputFileStack.setVolumeChunk(False)
                        leadOutputName, trailOutputName, nDigitsExpected = self.outputFileStack.fileStackInfo(outputBasename)
                    else:
                        self.outputFileStack.setVolumeChunk(True)

                print("Running image processing pipeline.")
                for i in range(self.inputFileStack.nSlices):
                    progress = 100*(float(i+1)/float(self.inputFileStack.nSlices))

                    print("\rImage {}/{} ({:0.1f}%)  \r".format((i+1), self.inputFileStack.nSlices, progress), end='')

                    if saveOutputFiles:
                        # Append if output target is a volume chunk:
                        appendMode = False
                        if self.outputFileStack.isVolumeChunk():
                            outputPath = generalOutputName
                            if (i>0):
                                appendMode = True
                        else:
                            fileNameDigit = i
                            if len(self.inputFileStack.fileNumbers) > 0:
                                if len(self.inputFileStack.fileNumbers) > i:
                                    fileNameDigit = self.inputFileStack.fileNumbers[i]

                            outputPath = "{folder}/{lead}{digits:{fill}{nDigits}}{trail}".format(folder=outputFolder, lead=leadOutputName, digits=fileNameDigit, fill='0', nDigits=nDigitsExpected, trail=trailOutputName)

                            # Check if file already exists:
                            if os.path.exists(outputPath):
                                if self.outputFileStack.isVolumeChunk():
                                    if overwrite is False:
                                        # If we don't want to overwrite volume
                                        # chunks, we need to break the loop
                                        # if the volume chunk already exists.
                                        nImagesSkipped = self.inputFileStack.nSlices
                                        break
                                else:
                                    # Output stack is not a volume:
                                    if overwrite is False:
                                        # Skip this image if it already exists
                                        # and overwrite is not allowed.
                                        nImagesSkipped += 1
                                        continue

                    image = self.inputFileStack.getImage(index=i, outputFile=outputFiles)

                    # Run through processing steps:
                    for step in self.processingSteps:
                        image = step.run(image)
                        if image is None:
                            raise Exception("Step {i} did not return a valid image from its run() method.".format(i=step.getIdentifier()))

                    if saveOutputFiles:
                        image.save(filename=outputPath, appendChunk=appendMode)

                    nImagesProcessed += 1

                print("Image {}/{} (100%)  ".format((i+1), self.inputFileStack.nSlices))

            else:
                log("No projection file(s) found that match the given name pattern.")

            if nImagesProcessed == 1:
                summary = f"{nImagesProcessed} image file processed"
            else:
                summary = f"{nImagesProcessed} image files processed"

            if nImagesSkipped > 0:
                summary += f", {nImagesSkipped} skipped because they already exist."

            log(f"{summary}       ")

            #if not saveOutputFiles:
            #    log("No output images were saved.")
        else:
            log("Nothing to do. The pipeline has no input files.")

Methods

def addStep(self, step)

Add a processing step to the pipeline.

Parameters

step : Step

 

Expand source code

def addStep(self, step):
    """Add a processing step to the pipeline.

    Parameters
    ----------
    step : ctsimu.processing.step.Step
    """
    if isinstance(step, Step):
        step.setPipeline(self)
        self.processingSteps.append(step)
    else:
        raise Exception("Failed to add processing step. Not a valid type of processing step: {}".format(step))

def run(self, overwrite: bool = True)

Run the processing pipeline with its current configuration.

Parameters

overwrite : bool

Overwrite existing image files?

Default value: True

Expand source code

def run(self, overwrite:bool=True):
    """Run the processing pipeline with its current configuration.

    Parameters
    ----------
    overwrite : bool
        Overwrite existing image files?

        Default value: `True`
    """
    if self.inputFileStack is not None:
        nImagesProcessed = 0
        nImagesSkipped   = 0

        # Build stack if it hasn't been built yet:
        if not self.inputFileStack.built:
            self.inputFileStack.buildStack()

        saveOutputFiles = False
        if isinstance(self.outputFileStack, ImageStack):
            saveOutputFiles = True

            # Set output parameters to input parameters if no others given:
            if self.outputFileStack.getFileDataType() is None:
                self.outputFileStack.setFileDataType(self.inputFileStack.getFileDataType())

            if self.outputFileStack.getFileByteOrder() is None:
                self.outputFileStack.setFileByteOrder(self.inputFileStack.getFileByteOrder())

        # Treat projection files
        if self.inputFileStack.nSlices > 0:
            outputFiles = None               

            if saveOutputFiles:
                outputFiles = self.outputFileStack.files
                generalOutputName = self.outputFileStack.getFilename()
                outputFolder   = os.path.dirname(generalOutputName)
                outputBasename = os.path.basename(generalOutputName)

                if outputFolder == "" or outputFolder is None:
                    outputFolder = "."

                if '%' in outputBasename:
                    self.outputFileStack.setVolumeChunk(False)
                    leadOutputName, trailOutputName, nDigitsExpected = self.outputFileStack.fileStackInfo(outputBasename)
                else:
                    self.outputFileStack.setVolumeChunk(True)

            print("Running image processing pipeline.")
            for i in range(self.inputFileStack.nSlices):
                progress = 100*(float(i+1)/float(self.inputFileStack.nSlices))

                print("\rImage {}/{} ({:0.1f}%)  \r".format((i+1), self.inputFileStack.nSlices, progress), end='')

                if saveOutputFiles:
                    # Append if output target is a volume chunk:
                    appendMode = False
                    if self.outputFileStack.isVolumeChunk():
                        outputPath = generalOutputName
                        if (i>0):
                            appendMode = True
                    else:
                        fileNameDigit = i
                        if len(self.inputFileStack.fileNumbers) > 0:
                            if len(self.inputFileStack.fileNumbers) > i:
                                fileNameDigit = self.inputFileStack.fileNumbers[i]

                        outputPath = "{folder}/{lead}{digits:{fill}{nDigits}}{trail}".format(folder=outputFolder, lead=leadOutputName, digits=fileNameDigit, fill='0', nDigits=nDigitsExpected, trail=trailOutputName)

                        # Check if file already exists:
                        if os.path.exists(outputPath):
                            if self.outputFileStack.isVolumeChunk():
                                if overwrite is False:
                                    # If we don't want to overwrite volume
                                    # chunks, we need to break the loop
                                    # if the volume chunk already exists.
                                    nImagesSkipped = self.inputFileStack.nSlices
                                    break
                            else:
                                # Output stack is not a volume:
                                if overwrite is False:
                                    # Skip this image if it already exists
                                    # and overwrite is not allowed.
                                    nImagesSkipped += 1
                                    continue

                image = self.inputFileStack.getImage(index=i, outputFile=outputFiles)

                # Run through processing steps:
                for step in self.processingSteps:
                    image = step.run(image)
                    if image is None:
                        raise Exception("Step {i} did not return a valid image from its run() method.".format(i=step.getIdentifier()))

                if saveOutputFiles:
                    image.save(filename=outputPath, appendChunk=appendMode)

                nImagesProcessed += 1

            print("Image {}/{} (100%)  ".format((i+1), self.inputFileStack.nSlices))

        else:
            log("No projection file(s) found that match the given name pattern.")

        if nImagesProcessed == 1:
            summary = f"{nImagesProcessed} image file processed"
        else:
            summary = f"{nImagesProcessed} image files processed"

        if nImagesSkipped > 0:
            summary += f", {nImagesSkipped} skipped because they already exist."

        log(f"{summary}       ")

        #if not saveOutputFiles:
        #    log("No output images were saved.")
    else:
        log("Nothing to do. The pipeline has no input files.")

def setInputFileStack(self, inputFileStack)

Set the input file stack.

Parameters

inputFileStack : ImageStack or str

A string or an ImageStack object that specifies the path of the input image file(s).

Expand source code

def setInputFileStack(self, inputFileStack):
    """Set the input file stack.

    Parameters
    ----------
    inputFileStack : ctsimu.image.ImageStack or str
        A string or an `ctsimu.image.ImageStack` object that specifies
        the path of the input image file(s).
    """
    self.inputFileStack = createImageStack(inputFileStack)

def setOutputFileStack(self, outputFileStack)

Set the output file parameters.

Parameters

outputFileStack : ImageStack or str

A string or an ImageStack object that specifies the path of the output image file(s).

Expand source code

def setOutputFileStack(self, outputFileStack):
    """Set the output file parameters.

    Parameters
    ----------
    outputFileStack : ctsimu.image.ImageStack or str
        A string or an `ctsimu.image.ImageStack` object that specifies
        the path of the output image file(s).
    """
    self.outputFileStack = createImageStack(outputFileStack)

def step(self, i: int)

Return step at position i in the pipeline.

Parameters

i : int

Step index (starting at zero).

Expand source code

def step(self, i:int):
    """Return step at position `i` in the pipeline.

    Parameters
    ----------
    i : int
        Step index (starting at zero).
    """

    if i < len(self.processingSteps):
        return self.processingSteps[i]
    else:
        raise Exception("Processing Pipeline: Requested processing step id (#{i}) exceeds number of stored processing steps ({n}).".format(i=i, n=len(self.processingSteps)))