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mihmih
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Merge pull request #1 from chaselgrove/dft
Dft
2 parents 9023c4d + f7fb061 commit 93fef75

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+64
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+64
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‎nibabel/dft.py

Lines changed: 64 additions & 114 deletions
Original file line numberDiff line numberDiff line change
@@ -17,34 +17,6 @@
1717
import sqlite3
1818
import dicom
1919

20-
_study_instance_uid_tag = dicom.tag.Tag(0x0020, 0x000d)
21-
_study_date_tag = dicom.tag.Tag(0x0008, 0x0020)
22-
_study_time_tag = dicom.tag.Tag(0x0008, 0x0030)
23-
_study_comments_tag = dicom.tag.Tag(0x0032, 0x4000)
24-
25-
_series_instance_uid_tag = dicom.tag.Tag(0x0020, 0x000e)
26-
_series_number_tag = dicom.tag.Tag(0x0020, 0x0011)
27-
_series_description_tag = dicom.tag.Tag(0x0008, 0x103e)
28-
_rows_tag = dicom.tag.Tag(0x0028, 0x0010)
29-
_columns_tag = dicom.tag.Tag(0x0028, 0x0011)
30-
_bits_allocated_tag = dicom.tag.Tag(0x0028, 0x0100)
31-
_bits_stored_tag = dicom.tag.Tag(0x0028, 0x0101)
32-
33-
_patients_name_tag = dicom.tag.Tag(0x0010, 0x0010)
34-
_patient_id_tag = dicom.tag.Tag(0x0010, 0x0020)
35-
_patients_birth_date_tag = dicom.tag.Tag(0x0010, 0x0030)
36-
_patients_sex_tag = dicom.tag.Tag(0x0010, 0x0040)
37-
38-
_sop_instance_uid_tag = dicom.tag.Tag(0x0008, 0x0018)
39-
_instance_number_tag = dicom.tag.Tag(0x0020, 0x0013)
40-
41-
_pixel_spacing_tag = dicom.tag.Tag(0x0028, 0x0030)
42-
_image_position_tag = dicom.tag.Tag(0x0020, 0x0032)
43-
_image_orientation_tag = dicom.tag.Tag(0x0020, 0x0037)
44-
_spacing_between_slices_tag = dicom.tag.Tag(0x0018, 0x0088)
45-
46-
_pixel_data_tag = dicom.tag.Tag(0x7fe0, 0x0010)
47-
4820
class DFTError(Exception):
4921
"base class for DFT exceptions"
5022

@@ -177,21 +149,21 @@ def as_nifti(self):
177149
d1 = self.storage_instances[0].dicom()
178150
dn = self.storage_instances[-1].dicom()
179151

180-
pdi = d1[_pixel_spacing_tag].value[0]
181-
pdj = d1[_pixel_spacing_tag].value[1]
182-
pdk = d1[_spacing_between_slices_tag].value
152+
pdi = d1.PixelSpacing[0]
153+
pdj = d1.PixelSpacing[0]
154+
pdk = d1.SpacingBetweenSlices
183155

184-
cosi = d1[_image_orientation_tag].value[0:3]
156+
cosi = d1.ImageOrientationPatient[0:3]
185157
cosi[0] = -1 * cosi[0]
186158
cosi[1] = -1 * cosi[1]
187-
cosj = d1[_image_orientation_tag].value[3:6]
159+
cosj = d1.ImageOrientationPatient[3:6]
188160
cosj[0] = -1 * cosj[0]
189161
cosj[1] = -1 * cosj[1]
190162

191-
pos_1 = numpy.array(d1[_image_position_tag].value)
163+
pos_1 = numpy.array(d1.ImagePositionPatient)
192164
pos_1[0] = -1 * pos_1[0]
193165
pos_1[1] = -1 * pos_1[1]
194-
pos_n = numpy.array(dn[_image_position_tag].value)
166+
pos_n = numpy.array(dn.ImagePositionPatient)
195167
pos_n[0] = -1 * pos_n[0]
196168
pos_n[1] = -1 * pos_n[1]
197169
cosk = pos_n - pos_1
@@ -378,90 +350,68 @@ def _update_dir(c, dir, files, studies, series, storage_instances):
378350
c.execute(query, (mtime, si_uid, dir, fname))
379351
return
380352

381-
def _update_file(c, dir, fname, studies, series, storage_instances):
353+
def _update_file(c, path, fname, studies, series, storage_instances):
382354
try:
383-
do = dicom.read_file('%s/%s' % (dir, fname))
384-
# do = dicom.read_file('%s/%s' % (dir, fname), stop_before_pixels=True)
385-
study_uid = do[_study_instance_uid_tag].value
386-
study_date = do[_study_date_tag].value
387-
study_time = do[_study_time_tag].value
388-
try:
389-
study_comments = do[_study_comments_tag].value
390-
except KeyError:
391-
study_comments = ''
392-
patient_name = do[_patients_name_tag].value
393-
patient_id = do[_patient_id_tag].value
394-
patient_birth_date = do[_patients_birth_date_tag].value
395-
patient_sex = do[_patients_sex_tag].value
396-
series_uid = do[_series_instance_uid_tag].value
397-
series_number = do[_series_number_tag].value
398-
series_description = do[_series_description_tag].value
399-
series_rows = int(do[_rows_tag].value)
400-
series_columns = int(do[_columns_tag].value)
401-
series_bits_allocated = int(do[_bits_allocated_tag].value)
402-
series_bits_stored = int(do[_bits_stored_tag].value)
403-
instance_number = int(do[_instance_number_tag].value)
404-
storage_instance_uid = do[_sop_instance_uid_tag].value
405-
# except Exception, data:
406-
# print 'exc', type(data), data, str(data)
407-
# return None
355+
do = dicom.read_file('%s/%s' % (path, fname))
408356
except dicom.filereader.InvalidDicomError:
409357
print ' not a DICOM file'
410358
return None
411-
except KeyError, data:
412-
print ' missing tag %s' % str(data)
413-
return None
414-
except Exception, data:
415-
print ' error: %s' % str(data)
359+
try:
360+
study_comments = do.StudyComments
361+
except AttributeError:
362+
study_comments = ''
363+
try:
364+
print ' storage instance %s' % str(do.SOPInstanceUID)
365+
if str(do.StudyInstanceUID) not in studies:
366+
query = """INSERT INTO study (uid,
367+
date,
368+
time,
369+
comments,
370+
patient_name,
371+
patient_id,
372+
patient_birth_date,
373+
patient_sex)
374+
VALUES (?, ?, ?, ?, ?, ?, ?, ?)"""
375+
params = (str(do.StudyInstanceUID),
376+
do.StudyDate,
377+
do.StudyTime,
378+
study_comments,
379+
do.PatientsName,
380+
do.PatientID,
381+
do.PatientsBirthDate,
382+
do.PatientsSex)
383+
c.execute(query, params)
384+
studies.append(str(do.StudyInstanceUID))
385+
if str(do.SeriesInstanceUID) not in series:
386+
query = """INSERT INTO series (uid,
387+
study,
388+
number,
389+
description,
390+
rows,
391+
columns,
392+
bits_allocated,
393+
bits_stored)
394+
VALUES (?, ?, ?, ?, ?, ?, ?, ?)"""
395+
params = (str(do.SeriesInstanceUID),
396+
str(do.StudyInstanceUID),
397+
do.SeriesNumber,
398+
do.SeriesDescription,
399+
do.Rows,
400+
do.Columns,
401+
do.BitsAllocated,
402+
do.BitsStored)
403+
c.execute(query, params)
404+
series.append(str(do.SeriesInstanceUID))
405+
if str(do.SOPInstanceUID) not in storage_instances:
406+
query = """INSERT INTO storage_instance (uid, instance_number, series)
407+
VALUES (?, ?, ?)"""
408+
params = (str(do.SOPInstanceUID), do.InstanceNumber, str(do.SeriesInstanceUID))
409+
c.execute(query, params)
410+
storage_instances.append(str(do.SOPInstanceUID))
411+
except AttributeError, data:
412+
print ' %s' % str(data)
416413
return None
417-
print ' storage instance %s' % storage_instance_uid
418-
if study_uid not in studies:
419-
query = """INSERT INTO study (uid,
420-
date,
421-
time,
422-
comments,
423-
patient_name,
424-
patient_id,
425-
patient_birth_date,
426-
patient_sex)
427-
VALUES (?, ?, ?, ?, ?, ?, ?, ?)"""
428-
params = (study_uid,
429-
study_date,
430-
study_time,
431-
study_comments,
432-
patient_name,
433-
patient_id,
434-
patient_birth_date,
435-
patient_sex)
436-
c.execute(query, params)
437-
studies.append(study_uid)
438-
if series_uid not in series:
439-
query = """INSERT INTO series (uid,
440-
study,
441-
number,
442-
description,
443-
rows,
444-
columns,
445-
bits_allocated,
446-
bits_stored)
447-
VALUES (?, ?, ?, ?, ?, ?, ?, ?)"""
448-
params = (series_uid,
449-
study_uid,
450-
series_number,
451-
series_description,
452-
series_rows,
453-
series_columns,
454-
series_bits_allocated,
455-
series_bits_stored)
456-
c.execute(query, params)
457-
series.append(series_uid)
458-
if storage_instance_uid not in storage_instances:
459-
query = """INSERT INTO storage_instance (uid, instance_number, series)
460-
VALUES (?, ?, ?)"""
461-
params = (storage_instance_uid, instance_number, series_uid)
462-
c.execute(query, params)
463-
storage_instances.append(storage_instance_uid)
464-
return storage_instance_uid
414+
return str(do.SOPInstanceUID)
465415

466416
def clear_cache():
467417
with _db_change() as c:

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