dicomfs fixes regarding encoding and other bits.

chaselgrove · mih · commit e8e70cc755cc · 2011-09-07T21:31:35.000+02:00
(communicated via email)
diff --git a/bin/dicomfs b/bin/dicomfs
@@ -7,20 +7,22 @@ import os
 import stat
 import errno
 import time
+import locale
 import fuse
 import dft
 
 uid = os.getuid()
 gid = os.getgid()
+encoding = locale.getdefaultlocale()[1]
 
 fuse.fuse_python_api = (0, 2)
 
 class FileHandle:
 
 	def __init__(self, fno):
 		self.fno = fno
-#		self.keep_cache = True
-#		self.direct_io = True
+		self.keep_cache = False
+		self.direct_io = False
 		return
 
 	def __str__(self):
@@ -36,8 +38,7 @@ class DICOMFS(fuse.Fuse):
 	def get_paths(self):
 		paths = {}
 		for study in dft.get_studies(self.dicom_path):
-			paths.setdefault(study.patient_name, {})
-			pd = paths[study.patient_name]
+			pd = paths.setdefault(study.patient_name_or_uid(), {})
 			patient_info = 'patient information\n'
 			patient_info = 'name: %s\n' % study.patient_name
 			patient_info += 'ID: %s\n' % study.patient_id
@@ -170,7 +171,7 @@ if len(sys.argv) != 3:
 
 fs = DICOMFS(dash_s_do='setsingle')
 fs.parse(['-f', '-s', sys.argv[2]])
-fs.dicom_path = sys.argv[1]
+fs.dicom_path = sys.argv[1].decode(encoding)
 try:
 	fs.main()
 except fuse.FuseError:
diff --git a/nibabel/dft.py b/nibabel/dft.py
@@ -88,6 +88,11 @@ def __getattribute__(self, name):
 			self.series = val
 		return val
 
+	def patient_name_or_uid(self):
+		if self.patient_name == '':
+			return self.uid
+		return self.patient_name
+
 class _Series(object):
 
 	def __init__(self, d):
@@ -372,7 +377,10 @@ def _update_file(c, dir, fname, studies, series, storage_instances):
 		study_uid = do[_study_instance_uid_tag].value
 		study_date = do[_study_date_tag].value
 		study_time = do[_study_time_tag].value
-		study_comments = do[_study_comments_tag].value
+		try:
+			study_comments = do[_study_comments_tag].value
+		except KeyError:
+			study_comments = ''
 		patient_name = do[_patients_name_tag].value
 		patient_id = do[_patient_id_tag].value
 		patient_birth_date = do[_patients_birth_date_tag].value
@@ -386,10 +394,19 @@ def _update_file(c, dir, fname, studies, series, storage_instances):
 		series_bits_stored = int(do[_bits_stored_tag].value)
 		instance_number = int(do[_instance_number_tag].value)
 		storage_instance_uid = do[_sop_instance_uid_tag].value
+#	except Exception, data:
+#		print 'exc', type(data), data, str(data)
+#		return None
 	except dicom.filereader.InvalidDicomError:
+		print '        not a DICOM file'
+		return None
+	except KeyError, data:
+		print '        missing tag %s' % str(data)
 		return None
-	except KeyError:
+	except Exception, data:
+		print '        error: %s' % str(data)
 		return None
+	print '        storage instance %s' % storage_instance_uid
 	if study_uid not in studies:
 		query = """INSERT INTO study (uid, 
 		                              date, 
@@ -477,6 +494,7 @@ def clear_cache():
 )
 
 _db_fname = '%s/dft.%d.sqlite' % (tempfile.gettempdir(), os.getuid())
+print 'db is %s' % _db_fname
 _db = sqlite3.connect(_db_fname, check_same_thread=False)
 
 with _db_change() as c:
diff --git a/tools/data.wsgi b/tools/data.wsgi
@@ -55,15 +55,15 @@ def handler(environ):
 def index(environ):
 	patients = {}
 	for s in dft.get_studies(base_dir):
-		patients.setdefault(s.patient_name, []).append(s)
+		patients.setdefault(s.patient_name_or_uid(), []).append(s)
 	output = ''
 	output += '<html><head><title>data</title></head>\n'
 	output += '<body>\n'
 	output += 'Home\n'
 	output += '<br />\n'
 	output += '<br />\n'
 	for p in sorted(patients):
-		output += 'Patient name: <a href="%s/">%s</a>\n' % (urllib.quote(p.encode('utf-8')), html_unicode(p))
+		output += 'Patient: <a href="%s/">%s</a>\n' % (urllib.quote(p.encode('utf-8')), html_unicode(p))
 		output += '<br />\n'
 		if len(patients[p]) == 1:
 			output += '1 study\n'
@@ -89,14 +89,14 @@ def html_unicode(u):
 	return cgi.escape(u.encode('utf-8'))
 
 def patient(patient):
-	studies = [ s for s in dft.get_studies() if s.patient_name == patient ]
+	studies = [ s for s in dft.get_studies() if s.patient_name_or_uid() == patient ]
 	if len(studies) == 0:
 		raise HandlerError('404 Not Found', 'patient %s not found\n' % patient)
 	studies.sort(study_cmp)
 	output = ''
 	output += '<html><head><title>data</title></head>\n'
 	output += '<body>\n'
-	output += '<a href="../">Home</a> -&gt; Patient %s\n' % html_unicode(studies[0].patient_name)
+	output += '<a href="../">Home</a> -&gt; Patient %s\n' % html_unicode(studies[0].patient_name_or_uid())
 	output += '<br />\n'
 	output += '<br />\n'
 	output += 'Patient name: %s\n' % html_unicode(studies[0].patient_name)
@@ -123,7 +123,7 @@ def patient(patient):
 def patient_date_time(patient, date_time):
 	study = None
 	for s in dft.get_studies():
-		if s.patient_name != patient:
+		if s.patient_name_or_uid() != patient:
 			continue
 		if date_time != '%s_%s' % (s.date, s.time):
 			continue
@@ -134,10 +134,10 @@ def patient_date_time(patient, date_time):
 	output = ''
 	output += '<html><head><title>data</title></head>\n'
 	output += '<body>\n'
-	output += '<a href="../../">Home</a> -&gt; <a href="../../%s/">Patient %s</a> -&gt; Study %s %s\n' % (urllib.quote(study.patient_name), html_unicode(study.patient_name), html_unicode(study.date), html_unicode(study.time))
+	output += '<a href="../../">Home</a> -&gt; <a href="../../%s/">Patient %s</a> -&gt; Study %s %s\n' % (urllib.quote(study.patient_name_or_uid()), html_unicode(study.patient_name_or_uid()), html_unicode(study.date), html_unicode(study.time))
 	output += '<br />\n'
 	output += '<br />\n'
-	output += 'Patient name: <a href="/../%s/">%s</a>\n' % (urllib.quote(study.patient_name), html_unicode(study.patient_name))
+	output += 'Patient name: <a href="/../%s/">%s</a>\n' % (urllib.quote(study.patient_name_or_uid()), html_unicode(study.patient_name))
 	output += '<br />\n'
 	output += 'Study UID: %s\n' % html_unicode(study.uid)
 	output += '<br />\n'
@@ -167,7 +167,7 @@ def patient_date_time(patient, date_time):
 def nifti(patient, date_time, scan):
 	study = None
 	for s in dft.get_studies():
-		if s.patient_name != patient:
+		if s.patient_name_or_uid() != patient:
 			continue
 		if date_time != '%s_%s' % (s.date, s.time):
 			continue
@@ -188,7 +188,7 @@ def nifti(patient, date_time, scan):
 def png(patient, date_time, scan):
 	study = None
 	for s in dft.get_studies():
-		if s.patient_name != patient:
+		if s.patient_name_or_uid() != patient:
 			continue
 		if date_time != '%s_%s' % (s.date, s.time):
 			continue
@@ -209,7 +209,6 @@ def png(patient, date_time, scan):
 
 if __name__ == '__main__':
 	import wsgiref.simple_server
-	server_prefix = ''
 	httpd = wsgiref.simple_server.make_server('', 8080, application)
 	httpd.serve_forever()
 
