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fix dicom example

This commit is contained in:
John Cupitt 2017-04-05 14:37:17 +01:00
parent 28693c060b
commit a0f420ea7e
1 changed files with 40 additions and 47 deletions
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doc/Examples.md
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@ -257,77 +257,70 @@ hard to find the one you want.
This utility copies files to a single flat directory, naming them using This utility copies files to a single flat directory, naming them using
fields from the DICOM header. You can actually find stuff! Useful. fields from the DICOM header. You can actually find stuff! Useful.
``` python ```python
#!/usr/bin/python #!/usr/bin/env python
import sys import sys
import re import re
import os import os
import shutil import shutil
from vipsCC import * import gi
gi.require_version('Vips', '8.0')
from gi.repository import Vips
if len (sys.argv) != 3: if len(sys.argv) != 3:
print 'rename DICOM files using tags from the header' print 'rename DICOM files using tags from the header'
print 'usage:' sys.exit(1)
print '\t%s srcdir destdir' % sys.argv[0]
print 'the directory tree below srcdir is searched, all files are'
print 'renamed and put into destdir in a flat list'
sys.exit (1)
srcdir = sys.argv[1] srcdir = sys.argv[1]
destdir = sys.argv[2] destdir = sys.argv[2]
if not os.access (destdir, os.F_OK | os.R_OK | os.W_OK | os.X_OK): if not os.access(destdir, os.F_OK | os.R_OK | os.W_OK | os.X_OK):
os.mkdir (destdir) os.mkdir(destdir)
def get_field (vim, field): def get_field(vim, field):
result = vim.meta_get_string (field) result = vim.get_value(field)
# remove any \n etc. # remove any \n etc.
result = re.sub ("\n", "", result) result = re.sub("\n", "", result)
# remove any leading or trailing spaces # remove any leading or trailing spaces
result = re.sub (" $", "", result) result = re.sub(" $", "", result)
result = re.sub ("^ ", "", result) result = re.sub("^ ", "", result)
return result return result
id_name = "magick-dcm:Patient'sID"
modality_name = "magick-dcm:Modality" modality_name = "magick-dcm:Modality"
series_name = "magick-dcm:SeriesNumber" series_name = "magick-dcm:SeriesNumber"
instance_name = "magick-dcm:Instance(formerlyImage)Number" instance_name = "magick-dcm:Instance(formerlyImage)Number"
date_name = "magick-dcm:ImageDate" date_name = "magick-dcm:ImageDate"
n_processed = 0 for(dirpath, dirnames, filenames) in os.walk(srcdir):
for file in filenames:
path = os.path.join(dirpath, file)
for (dirpath, dirnames, filenames) in os.walk (srcdir): try:
for file in filenames: vim = Vips.Image.new_from_file(path)
path = os.path.join (dirpath, file) except Vips.Error, e:
print 'unable to open', path
print e
continue
try: try:
vim = VImage.VImage (path) modality = get_field(vim, modality_name)
except VError.VError, e: series = get_field(vim, series_name)
print 'unable to open', path instance = get_field(vim, instance_name)
continue date = get_field(vim, date_name)
except Vips.Error, e:
print 'unable to get fields from header', path
print e
continue
try: match = re.match("(\d\d\d\d)(\d\d)(\d\d)", date)
id = get_field (vim, id_name) date = match.group(1) + "." + match.group(2) + "." + match.group(3)
modality = get_field (vim, modality_name)
series = get_field (vim, series_name)
instance = get_field (vim, instance_name)
date = get_field (vim, date_name)
except VError.VError, e:
print 'unable to get fields from header', path
continue
match = re.match ("(\d\d\d\d)(\d\d)(\d\d)", date) newname = "lan." + modality + "." + instance + "." + date + ".IMA"
date = match.group (1) + "." + match.group (2) + "." + match.group (3)
newname = id + "." + modality + "." + series + "." + instance + "." + date + ".IMA"
shutil.copyfile(path, os.path.join (destdir, newname)) shutil.copyfile(path, os.path.join(destdir, newname))
n_processed += 1
print '\t(%d files processed)' % n_processed
``` ```