Python images.Images类代码示例

    def qaSupplier(self):
        """Create and supply images for the report generated by qa task

        """
        qaImages = Images()
        softwareName = 'dipy'

        #Produce tensor ellipsoids png image
        rgb = self.getImage('dwi', ['tensor', 'rgb'])
        cc = self.getMaskingImage('aparc_aseg', ['253','mask'])
        ellipsoidsPng = self.buildName(rgb, 'ellipsoids', 'png')
        self.tensorPng(self.__fit, cc, ellipsoidsPng)
        qaImages.extend(Images((ellipsoidsPng, 'Tensor ellipsoids in a part of the CC')))

        #Get images
        mask = self.getRegistrationImage('mask', 'resample')

        #Build qa images
        tags = (
            #(['tensor', 'rgb'], 'RGB map'),
            ('fa', 'Fractional anisotropy'),
            ('ad', 'Axial Diffusivity'),
            ('md', 'Mean Diffusivity'),
            ('rd', 'Radial Diffusivity'),
            )

        for postfix, description in tags:
            image = self.getImage('dwi', postfix)
            if image:
                qaImage = self.buildName(image, softwareName, 'png')
                self.slicerPng(image, qaImage, boundaries=mask)
                qaImages.extend(Images((qaImage, description)))

        return qaImages

    def qaSupplier(self):
        """Create and supply images for the report generated by qa task

        """
        qaImages = Images()
        softwareName = 'mrtrix'

        #Get images
        mask = self.getRegistrationImage('mask', 'resample')

        #Build qa images
        tags = (
            ('nufo', 5, 'nufo'),
            ('afd', 5,'afd')
            )

        for postfix, vmax, description in tags:
            image = self.getImage('dwi', postfix)
            if image:
                imageQa = self.plot3dVolume(
                        image, fov=mask, vmax=vmax,
                        colorbar=True, postfix=softwareName)
                qaImages.append((imageQa, description))

        return qaImages

    def implement(self):

        self.info("Build directories structure for subject: {}".format(os.path.basename(self.workingDir)))
        #@TODO add description to that struct
        images = Images((self.getSubjectImage('anat'), ""),
                       (self.getSubjectImage('dwi'), ""),
                       (self.getSubjectImage('mag',), ""),
                       (self.getSubjectImage('phase'), ""),
                       (self.getSubjectImage('aparc_aseg'), ""),
                       (self.getSubjectImage('anat', 'freesurfer'), ""),
                       (self.getSubjectImage('lh_ribbon'), ""),
                       (self.getSubjectImage('rh_ribbon'), ""),
                       (self.getSubjectImage('brodmann'), ""),
                       (self.getSubjectImage('b0_ap'), ""),
                       (self.getSubjectImage('b0_pa'), ""),
                       (self.getSubjectImage('grad', None, 'b'), ""),
                       (self.getSubjectImage('grad', None, 'bvals'), ""),
                       (self.getSubjectImage('grad', None, 'bvecs'), ""),
                       (self.getSubjectImage('tq_dict', None, 'qry'), ""),
                       (self.getSubjectImage('queries', None, 'qry'), ""),
                       (self.getSubjectImage('config', None, 'cfg'), ""),)

        for image, description in images.getData():
            if image:
                self.info("Found {} image: moving it to {} directory".format(description, image, self.workingDir))
                shutil.move(image, self.workingDir)

        directories = [os.path.join(self.subjectDir, directory) for directory in os.listdir(self.subjectDir) if os.path.isdir(os.path.join(self.subjectDir, directory))]
        for directory in directories:
            if mriutil.isAfreesurferStructure(directory):
                self.info("{} seem\'s a valid freesurfer structure: moving it to {} directory".format(directory, self.workingDir))
                shutil.move(directory, self.workingDir)

    def qaSupplier(self):
        """Create and supply images for the report generated by qa task

        """
        qaImages = Images()
        softwareName = 'fsl'

        #Get images
        mask = self.getRegistrationImage('mask', 'resample')

        #Build qa images
        tags = (
            ('fa', 0.7, 'Fractional anisotropy'),
            ('ad', 0.005, 'Axial Diffusivity'),
            ('md', 0.005, 'Mean Diffusivity'),
            ('rd', 0.005, 'Radial Diffusivity'),
            )

        for postfix, vmax, description in tags:
            image = self.getImage('dwi', postfix)
            if image:
                imageQa = self.plot3dVolume(
                        image, fov=mask, vmax=vmax,
                        colorbar=True, postfix=softwareName)
                qaImages.append((imageQa, description))

        #Build SSE image
        sse = self.getImage('dwi', 'sse')
        sseQa = self.plot3dVolume(
                sse, fov=mask, postfix=softwareName, colorbar=True)
        qaImages.append((sseQa, 'Sum of squared errors'))

        return qaImages

    def qaSupplier(self):
        """Create and supply images for the report generated by qa task

        """
        qaImages = Images()

        #Get images
        dwiNative = self.getPreparationImage('dwi')
        dwiCorrected = self.getCorrectionImage('dwi', 'corrected')
        dwiDenoised = self.getDenoisingImage('dwi', 'denoise')
        noiseMask = self.getImage('mask', ['corrected', 'noisemask'])
        ccMask = self.getImage('aparc_aseg', ['253', 'mask', 'downsample'])
        b0 = self.getCorrectionImage('b0', 'corrected')

        #Build qa images
        tags = (
            (dwiNative, 'Native'),
            (dwiDenoised, 'denoised'),
            (dwiCorrected, 'Corrected'),
            )
        for dwi, description in tags:
            if dwi:
                qaImages = self.__noiseAnalysis(dwi, noiseMask, ccMask, qaImages, description)

        #Build qa masks images
        tags = (
            (noiseMask, 'Noise mask'),
            (ccMask, 'Corpus callosum mask'),
            )
        for mask, description in tags:
            maskPng = self.buildName(mask, None, 'png')
            self.slicerPng(b0, maskPng, maskOverlay=mask, boundaries=mask)
            qaImages.append((maskPng, description))

        return qaImages

    def qaSupplier(self):
        """Create and supply images for the report generated by qa task

        """
        qaImages = Images()
        softwareName = 'mrtrix'

        #Set information
        information = "Estimation using WLS with {} iteration(s)".format(self.get('iter'))
        qaImages.setInformation(information)

        #Get images
        mask = self.getRegistrationImage('mask', 'resample')

        #Build qa images
        tags = (
            ('fa', 0.7, 'Fractional anisotropy'),
            ('ad', 0.005, 'Axial Diffusivity'),
            ('md', 0.005, 'Mean Diffusivity'),
            ('rd', 0.005, 'Radial Diffusivity'),
            )

        for postfix, vmax, description in tags:
            image = self.getImage('dwi', postfix)
            if image:
                imageQa = self.plot3dVolume(
                        image, fov=mask, vmax=vmax,
                        colorbar=True, postfix=softwareName)
                qaImages.append((imageQa, description))

        return qaImages

    def qaSupplier(self):
        """Create and supply images for the report generated by qa task

        """
        qaImages = Images()
        softwareName = 'dipy'

        #Get images
        mask = self.getRegistrationImage('mask', 'resample')

        #Build qa images
        tags = (
            ('fa', 'Fractional anisotropy'),
            ('ad', 'Axial Diffusivity'),
            ('md', 'Mean Diffusivity'),
            ('rd', 'Radial Diffusivity'),
            )

        for postfix, description in tags:
            image = self.getImage('dwi', postfix)
            if image:
                qaImage = self.buildName(image, softwareName, 'png')
                self.slicerPng(image, qaImage, boundaries=mask)
                qaImages.extend(Images((qaImage, description)))

        return qaImages

    def qaSupplier(self):
        """Create and supply images for the report generated by qa task

        """
        qaImages = Images()

        #Get images
        b0 = self.getUpsamplingImage('b0', 'upsample')
        whiteMatter = self.getImage("tt5", ["resample", "wm", "mask"])
        interfaceGmWm = self.getImage("tt5", ["register", "5tt2gmwmi"])
        area253 = self.getImage('aparc_aseg',['253','mask'])
        area1024 = self.getImage('aparc_aseg',['1024','mask'])

        #Build qa images
        tags = (
            (whiteMatter, 'resample white segmented mask'),
            #(interfaceGmWm, 'grey matter, white matter interface'),
            #(area253, 'area 253 from aparc_aseg atlas'),
            #(area1024, 'area 1024 from aparc_aseg atlas'),
            )
        for image, description in tags:
            qaImage = self.buildName(image, None, 'png')
            self.slicerPng(b0, qaImage, maskOverlay=image, boundaries=image)
            qaImages.extend(Images((qaImage, description)))

        return qaImages

    def qaSupplier(self):
        """Create and supply images for the report generated by qa task

        """
        qaImages = Images()

        # Get images
        dwiNative = self.getPreparationImage("dwi")
        dwiCorrected = self.getCorrectionImage("dwi", "corrected")
        dwiDenoised = self.getDenoisingImage("dwi", "denoise")
        noiseMask = self.getImage("mask", ["corrected", "noisemask"])
        ccMask = self.getImage("aparc_aseg", ["253", "mask", "downsample"])
        b0 = self.getCorrectionImage("b0", "corrected")

        # Build qa images
        tags = ((dwiNative, "Native"), (dwiDenoised, "denoised"), (dwiCorrected, "Corrected"))
        for dwi, description in tags:
            if dwi:
                qaImages = self.__noiseAnalysis(dwi, noiseMask, ccMask, qaImages, description)

        # Build qa masks images
        tags = ((noiseMask, "Noise mask"), (ccMask, "Corpus callosum mask"))
        for mask, description in tags:
            maskPng = self.buildName(mask, None, "png")
            self.slicerPng(b0, maskPng, maskOverlay=mask, boundaries=mask)
            qaImages.append((maskPng, description))

        return qaImages

    def qaSupplier(self):
        """Create and supply images for the report generated by qa task

        """
        qaImages = Images()

        information = "Warning: due to storage restriction, streamlines were " \
                      "downsampled. Even if there is no difference in structural " \
                      "connectivity, you should be careful before computing any " \
                      "metrics along these streamlines.\n To run toad without this " \
                      "downsampling, please refer to the documentation."

        if self.defaultQuery:
            # get images
            norm = self.getRegistrationImage("norm", "resample")
            self.__buildNameTractQuerierOutputs()
            # images production
            tags = (
                (self.queries[0],
                 'Corpus Callosum',
                 95, 60, 40, -80, 0, 160),
                (self.queries[1],
                 'Inferior Fronto Occipital tract left',
                 95, 80, 40, -90, 0, 90),
                (self.queries[2],
                 'Inferior Fronto Occipital tract right',
                 95, 80, 40, -90, 0, -90),
                (self.queries[3],
                 'inferior Longitudinal Fasciculus left',
                 95, 80, 40, -90, 0, 90),
                (self.queries[4],
                 'Inferior Longitudinal Fasciculus right',
                 95, 80, 40, -90, 0, -90),
                (self.queries[5],
                 'Uncinate Fasciculus left',
                 95, 80, 40, -90, 0, 90),
                (self.queries[6],
                 'Uncinate Fasciculus right',
                 95, 80, 40, -90, 0, -90),
                (self.queries[7],
                 'Corticospinal tract Left',
                 95, 80, 40, -90, 0, 160),
                (self.queries[8],
                 'Corticospinal tract right',
                 95, 80, 40, -90, 0, 200),
                )

            for data, description, xSlice, ySlice, zSlice, xRot, yRot, zRot in tags:
                if data:
                    imageQa = self.plotTrk(data, norm, None, xSlice, ySlice, zSlice, xRot, yRot, zRot)
                    qaImages.append((imageQa, description))
        else:
            information = """
            Because you didn't choose default queries and dictionnary,
            we are not able to create proper screenshots of the output bundles.
            """
        qaImages.setInformation(information)

        return qaImages

    def isDirty(self):

        images = Images()

        dwi = self.getUpsamplingImage('dwi', 'upsample')

        if mriutil.getNbDirectionsFromDWI(dwi) <= 45  and not self.get('forceHardi'):
            if 'deterministic' in self.get('algorithm'):
                images.append((
                    self.getImage('dwi', 'tensor_det', 'trk'),
                    "deterministic tensor connectome matrix from a streamlines"
                    ))

            if 'probabilistic' in self.get('algorithm'):
                images.append((
                    self.getImage('dwi', 'tensor_prob', 'trk'),
                    "probabilistic tensor connectome matrix from a streamlines"
                    ))

        else:
            images.append((
                    self.getImage('dwi', 'hardi_prob', 'trk'),
                    "tckgen hardi probabilistic streamlines tractography"
                    ))

            if self.get('sift'):
                images.append((
                    self.getImage('dwi', 'tcksift', 'trk'), 'tcksift'))

        return images

    def meetRequirement(self, result=True):

        #@TODO add gradient files validation and correct this function
        images = Images((self.getDenoisingImage("dwi", 'denoise'), 'denoised'),
                       (self.getCorrectionImage("dwi", 'corrected'), 'corrected'),
                       (self.getPreparationImage("dwi"), 'diffusion weighted'))

        if images.isNoImagesExists():
            self.warning("No proper dwi image found as requirement")
            result = False
        return result

    def meetRequirement(self, result = True):
        images = Images((self.getCorrectionImage("dwi", 'corrected'), 'corrected'),
                       (self.getPreparationImage("dwi"), 'diffusion weighted'))

        if not images.isAtLeastOneImageExists():
            return False

        images = Images((self.getParcellationImage('norm'), 'freesurfer normalize'),
                        (self.getParcellationImage('mask'), 'freesurfer mask'))

        return images

    def implement(self):

        self.info("Build directories structure for subject: {}".format(
            os.path.basename(self.workingDir)))
        #@TODO add description to that struct
        images = Images((self.getSubjectImage('anat'), ""),
                       (self.getSubjectImage('dwi'), ""),
                       (self.getSubjectImage('mag',), ""),
                       (self.getSubjectImage('phase'), ""),
                       (self.getSubjectImage('aparc_aseg'), ""),
                       (self.getSubjectImage('anat', 'freesurfer'), ""),
                       (self.getSubjectImage('lh_ribbon'), ""),
                       (self.getSubjectImage('rh_ribbon'), ""),
                       (self.getSubjectImage('brodmann'), ""),
                       (self.getSubjectImage('b0_ap'), ""),
                       (self.getSubjectImage('b0_pa'), ""),
                       (self.getSubjectImage('grad', None, 'b'), ""),
                       (self.getSubjectImage('grad', None, 'bvals'), ""),
                       (self.getSubjectImage('grad', None, 'bvecs'), ""),
                       (self.getSubjectImage('tq_dict', None, 'qry'), ""),
                       (self.getSubjectImage('queries', None, 'qry'), ""),
                       (self.getSubjectImage('config', None, 'cfg'), ""),)

        for image, description in images.getData():
            if image:
                self.info("Found {} image: moving it to {} directory".format(
                    description, image, self.workingDir))
                shutil.move(image, self.workingDir)

        directories = []
        for directory in os.listdir(self.subjectDir):
            target = os.path.join(self.subjectDir, directory)
            if os.path.isdir(target):
                directories.append(target)

        for directory in directories:
            if mriutil.isAfreesurferStructure(directory):
                self.info("{} seem\'s a valid freesurfer structure: moving it to {} directory".format(directory, self.workingDir))

                if os.path.islink(directory):
                    os.chdir(self.subjectDir)
                    # We need to chdir because `directory` is in
                    # `self.subjectDir` and we need `os.path.abspath` to
                    # work correctly
                    fsDirName = os.path.basename(directory)
                    linkto = os.path.abspath(os.readlink(directory))
                    newLinkto = os.path.relpath(linkto, self.workingDir)
                    newTarget = os.path.join(self.workingDir, fsDirName)
                    os.symlink(newLinkto, newTarget)
                    os.unlink(directory)
                    os.chdir(self.workingDir)
                else:
                    shutil.move(directory, self.workingDir)

    def meetRequirement(self):
        images = Images((self.getPreparationImage('dwi'), 'diffusion weighted'),
                        (self.getParcellationImage('norm'), 'freesurfer normalize'),
                        (self.getParcellationImage('mask'), 'freesurfer mask'),
                        (self.getPreparationImage('grad', None, 'bvals'), 'gradient .bvals encoding file'),
                        (self.getPreparationImage('grad', None, 'bvecs'), 'gradient .bvecs encoding file'),
                        (self.getPreparationImage('grad', None, 'b'), 'gradient .b encoding file'))

        #if fieldmap available
        if Images(self.getPreparationImage("mag") , self.getPreparationImage("phase")).isAllImagesExists():
            images.append((self.getParcellationImage('anat', 'freesurfer'),"freesurfer anatomical"))

        return images