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from datetime import datetime |
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from niprov.basefile import BaseFile |
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from niprov.libraries import Libraries |
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class DicomFile(BaseFile): |
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def __init__(self, location, **kwargs): |
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super(DicomFile, self).__init__(location, **kwargs) |
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self.libs = self.dependencies.getLibraries() |
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def inspect(self): |
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""" |
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Inspect the DICOM file attributes. |
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If a general AcquisitionDateTime attribute is not present, the |
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SeriesDate and SeriesTime will be used to set the :ref:`field-acquired` |
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provenance field. |
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Returns: |
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dict: Provenance for the inspected file. |
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""" |
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super(DicomFile, self).inspect() |
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img = self.libs.dicom.read_file(self.path) |
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self.provenance['subject'] = img.PatientID |
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self.provenance['protocol'] = img.SeriesDescription |
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self.provenance['seriesuid'] = img.SeriesInstanceUID |
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self.provenance['filesInSeries'] = [self.path] |
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self.provenance['duration'] = img.AcquisitionDuration |
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self.provenance['subject-position'] = img.PatientPosition |
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self.provenance['water-fat-shift'] = img[0x2001, 0x1022].value |
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if hasattr(img, 'NumberOfFrames'): |
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self.provenance['multiframeDicom'] = True |
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nframes = int(img.NumberOfFrames) |
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else: |
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self.provenance['multiframeDicom'] = False |
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nframes = len(self.provenance['filesInSeries']) |
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if hasattr(img, 'Rows'): |
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self.provenance['dimensions'] = [int(img.Rows), int(img.Columns), |
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nframes] |
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if hasattr(img, 'AcquisitionDateTime'): |
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acqstring = img.AcquisitionDateTime.split('.')[0] |
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dateformat = '%Y%m%d%H%M%S' |
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self.provenance['acquired'] = datetime.strptime(acqstring,dateformat) |
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else: |
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dateformat = '%Y%m%d' |
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acqdate = datetime.strptime(img.SeriesDate, dateformat) |
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acqtime = datetime.fromtimestamp(float(img.SeriesTime)).time() |
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combined = datetime.combine(acqdate, acqtime) |
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self.provenance['acquired'] = combined.replace(microsecond=0) |
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self.provenance['modality'] = 'MRI' |
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return self.provenance |
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def getSeriesId(self): |
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""" |
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Return the DICOM "SeriesInstanceUID" that all files in this series |
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have in common. |
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Returns: |
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str: A string uniquely identifying files belonging to this series. |
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""" |
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if not 'seriesuid' in self.provenance: |
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self.inspect() |
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return self.provenance['seriesuid'] |
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def mergeWith(self, img): |
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""" |
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Add a single DICOM file object to this series. |
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The file will be stored in provenance in the 'filesInSeries' list. |
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""" |
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self.provenance['filesInSeries'].append(img.path) |
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self._updateNfilesDependentFields() |
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self.status = 'series-new-file' |
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return self |
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def _updateNfilesDependentFields(self): |
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if (not self.provenance['multiframeDicom']) and 'dimensions' in self.provenance: |
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nfiles = len(self.provenance['filesInSeries']) |
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self.provenance['dimensions'][2] = nfiles |
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ilogue /
niprov
