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# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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# See COPYING file distributed along with the NiBabel package for the
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# copyright and license terms.
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### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
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# Copyright (C) 2011 Christian Haselgrove
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from nibabel import dft
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return cgi.escape(u.encode('utf-8'))
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# this is the directory containing the DICOM data, or None for all cached data
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base_dir = '/path/to/DICOM'
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template_env = jinja2.Environment(autoescape=True)
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template_env.filters['urlquote'] = urllib.quote
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index_template = """<html><head><title>data</title></head>
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{% for p in patients|sort %}
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Patient: <a href="{{ p|urlquote }}/">{{ p }}</a>
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{% if patients[p]|length == 1 %}
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{{ patients[p]|length }} studies
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patient_template = """<html><head><title>data</title></head>
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<a href="../">Home</a> -> Patient {{ studies[0].patient_name_or_uid() }}
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Patient name: {{ studies[0].patient_name }}
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Patient ID: {{ studies[0].patient_id }}
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Patient birth date: {{ studies[0].patient_birth_date }}
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Patient sex: {{ studies[0].patient_sex }}
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{% for s in studies %}
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<li><a href="{{ s.date|urlquote }}_{{ s.time|urlquote }}/">Study {{ s.uid }}</a></li>
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<li>Date: {{ s.date }}</li>
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<li>Time: {{ s.time }}</li>
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<li>Comments: {{ s.comments }}</li>
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<li>Series: {{ s.series|length }}</li>
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patient_date_time_template = """
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<html><head><title>data</title></head>
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<a href="../../">Home</a> -> <a href="../../{{ study.patient_name_or_uid() }}/">Patient {{ study.patient_name_or_uid() }}</a> -> Study {{ study.date}} {{ study.time }}
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Patient name: <a href="../../{{ study.patient_name_or_uid() }}/">{{ study.patient_name }}</a>
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Study UID: {{ study.uid }}
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Study date: {{ study.date }}
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Study time: {{ study.time }}
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Study comments: {{ study.comments }}
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{% if study.series|length == 0 %}
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{% for s in study.series %}
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<li>Series {{ s.number }} (<a href="{{ s.number }}/nifti">NIfTI</a>)</li>
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<li>Series UID: {{ s.uid }}</li>
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<li>Series description: {{ s.description }}</li>
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<li>Series dimensions: {{ s.rows }}x{{ s.columns }}x{{ s.storage_instances|length }}</li>
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<img src="{{ s.number }}/png" />
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def __init__(self, status, output):
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def application(environ, start_response):
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(status, c_type, output) = handler(environ)
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except HandlerError, exc:
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c_type = 'text/plain'
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(exc_type, exc_value, exc_traceback) = sys.exc_info()
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lines = traceback.format_exception(exc_type, exc_value, exc_traceback)
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status = '500 Internal Server Error'
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output = ''.join(lines)
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c_type = 'text/plain'
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response_headers = [('Content-Type', c_type),
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('Content-Length', str(len(output)))]
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if c_type == 'image/nifti':
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response_headers.append(('Content-Disposition', 'attachment; filename=image.nii'))
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start_response(status, response_headers)
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def handler(environ):
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if environ['PATH_INFO'] == '' or environ['PATH_INFO'] == '/':
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return ('200 OK', 'text/html', index(environ))
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parts = environ['PATH_INFO'].strip('/').split('/')
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return ('200 OK', 'text/html', patient(parts[0]))
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return ('200 OK', 'text/html', patient_date_time(parts[0], parts[1]))
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if parts[3] == 'nifti':
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return ('200 OK', 'image/nifti', nifti(parts[0], parts[1], parts[2]))
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elif parts[3] == 'png':
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return ('200 OK', 'image/png', png(parts[0], parts[1], parts[2]))
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raise HandlerError('404 Not Found', "%s not found\n" % environ['PATH_INFO'])
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for s in dft.get_studies(base_dir):
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patients.setdefault(s.patient_name_or_uid(), []).append(s)
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template = template_env.from_string(index_template)
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return template.render(patients=patients).encode('utf-8')
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def patient(patient):
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studies = [ s for s in dft.get_studies() if s.patient_name_or_uid() == patient ]
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if len(studies) == 0:
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raise HandlerError('404 Not Found', 'patient %s not found\n' % patient)
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studies.sort(study_cmp)
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template = template_env.from_string(patient_template)
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return template.render(studies=studies).encode('utf-8')
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def patient_date_time(patient, date_time):
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for s in dft.get_studies():
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if s.patient_name_or_uid() != patient:
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if date_time != '%s_%s' % (s.date, s.time):
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raise HandlerError, ('404 Not Found', 'study not found')
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template = template_env.from_string(patient_date_time_template)
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return template.render(study=study).encode('utf-8')
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def nifti(patient, date_time, scan):
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for s in dft.get_studies():
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if s.patient_name_or_uid() != patient:
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if date_time != '%s_%s' % (s.date, s.time):
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raise HandlerError, ('404 Not Found', 'study not found')
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for series in s.series:
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if series.number != scan:
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raise HandlerError, ('404 Not Found', 'series not found')
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return ser.as_nifti()
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def png(patient, date_time, scan):
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for s in dft.get_studies():
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if s.patient_name_or_uid() != patient:
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if date_time != '%s_%s' % (s.date, s.time):
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raise HandlerError, ('404 Not Found', 'study not found')
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for series in s.series:
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if series.number != scan:
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raise HandlerError, ('404 Not Found', 'series not found')
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index = len(ser.storage_instances) / 2
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return ser.as_png(index, True)
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if __name__ == '__main__':
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import wsgiref.simple_server
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httpd = wsgiref.simple_server.make_server('', 8080, application)
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httpd.serve_forever()
added
removed
tools/dicomfs.wsgi
