363 lines
12 KiB
Python
363 lines
12 KiB
Python
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import glob
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import re
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"""
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def parse_z1(s):
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'''
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0008 0005 10 | specific_character_set | CS | 1-n | "ISO_IR 192"
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'''
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pattern = '(?P<Grp>\d{4}) (?P<Elmt>\d{4})\s+(?P<Length>\d+) \|\s+(?P<Description>[^|]+?)\s+\| (?P<VR>..) \|\s+(?P<VM>\S+)\s+\|\s*(?P<Value>"[^|]*?"|\*[\s\S]+?Seq|[^\r]*)'
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r = re.compile(pattern)
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return [m.groupdict() for m in r.finditer(s)]
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def parse_z2(s):
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'''
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[ object, original_order ] = 1 ( 4, 4 )
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'''
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pattern = '\[ (.+?), (.+?) \] = (.+?) \( (.+?), (.+?) \)'
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return re.findall(pattern, s, re.MULTILINE)
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def parse_z(s):
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pattern = '(?P<Grp>\d{4}) (?P<Elmt>\d{4})\s+(?P<Length>\d+) \|\s+(?P<Description>[^|]+?)\s+\| (?P<VR>..) \|\s+(?P<VM>\S+)\s+\|\s*(?P<Value>"[^|]*?"|\*[\s\S]+?Seq|[^\r]*)'
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r = re.compile(pattern)
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ret1 = [m.groupdict() for m in r.finditer(s)]
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pattern = '\[ (.+?), (.+?) \] = (.+?) \( (.+?), (.+?) \)'
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ret2 = re.findall(pattern, s, re.MULTILINE)
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return ret1, ret2
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"""
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class IMPAX_Description:
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def __init__(self, s):
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pattern = '(?P<Grp>\d{4}) (?P<Elmt>\d{4})\s+(?P<Length>\d+) \|\s+(?P<Description>[^|]+?)\s+\| (?P<VR>..) \|\s+(?P<VM>\S+)\s+\|\s*(?P<Value>"[^|]*?"|\*[\s\S]+?Seq|[^\r]*)'
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r = re.compile(pattern)
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self.data1 = [m.groupdict() for m in r.finditer(s)]
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pattern = '\[ (.+?), (.+?) \] = (.+?) \( (.+?), (.+?) \)'
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self.data2 = re.findall(pattern, s, re.MULTILINE)
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self.data = {}
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for elm in self.data2:
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self.data[elm[1]] = elm[2].replace('"', '')
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for elm in self.data1:
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if '...' not in elm['Value']:
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self.data[elm['Description']] = elm['Value'].replace('"', '')
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# print self.data
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# exit()
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def dump(self):
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return self.data1, self.data2
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def get_old(self, s):
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for elm in self.data2:
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if elm[1] == s:
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return elm[2].replace('"', '')
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for elm in self.data1:
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if elm['Description'] == s:
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return elm['Value'].replace('"', '')
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raise NameError('%s not found' % s)
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def get(self, s):
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if s in self.data:
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# print s, self.data[s]
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return self.data[s]
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raise NameError('%s not found' % s)
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def keys(self):
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return self.data.keys()
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def __sub__(self, other):
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sdata = {}
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for k in self.data:
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if k not in other.data:
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# sdata[k] = (self.data[k], None)
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pass
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elif self.data[k] != other.data[k]:
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sdata[k] = (self.data[k], other.data[k])
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for k in other.data:
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if k not in self.data:
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# sdata[k] = (None, other.data[k])
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pass
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return sdata
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class IMPAX_Series_one:
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def __init__(self, path):
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self.path = path
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ztxt = '%s/z.txt' % (path)
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with open(ztxt, 'r') as myfile:
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data=myfile.read()
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self.Description = IMPAX_Description(data)
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def direction(self):
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import numpy as np
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image_orientation_patient = self.Description.get('image_orientation_patient').split('\\')
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image_position_patient = self.Description.get('image_position_patient').split('\\')
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dir = [round(float(a)) for a in image_orientation_patient]
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pos = map(float, image_position_patient)
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dir2 = (abs(np.array(dir[:3])+np.array(dir[3:]))-1)*pos
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dir2 = dir2 / np.linalg.norm(dir2)
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print self.path
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print image_orientation_patient
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print image_position_patient
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print dir
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print dir2
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return dir + dir2.tolist()
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def write(self, filename):
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import SimpleITK
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print self.Description.get('image_number')
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# print self.Description.get('referenced_image_sequence')
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# print self.Description.get('source_image_sequence')
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files = glob.glob("%s/*.jpg" % self.path)
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files.sort()
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sreader1 = SimpleITK.ImageSeriesReader()
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sreader1.SetFileNames(files)
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img = sreader1.Execute()
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pixel_spacing = self.Description.get('pixel_spacing').split('\\')
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try:
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slice_spacing = float(self.Description.get('slice_spacing'))
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except:
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slice_spacing = float(self.Description.get('slice_thickness'))
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img.SetDirection(self.direction())
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img.SetSpacing((float(pixel_spacing[0]), float(pixel_spacing[1]), slice_spacing))
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SimpleITK.WriteImage(img, filename)
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print img.GetDirection()
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print
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class IMPAX_Series:
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def __init__(self, path):
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self.DescriptionOrder = {}
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self.path = path
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files = glob.glob("%s/z*.txt" % self.path)
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for filename in files:
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# print filename
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m = re.search('z(.+).txt', filename)
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if m is None:
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continue
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f_number = int(m.group(1))
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print filename, f_number
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with open(filename, 'r') as myfile:
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data=myfile.read()
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d = IMPAX_Description(data)
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print d.get('image_number')
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d_number = int(d.get('image_number'))
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if d_number != f_number:
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raise NameError('File name: %s, Description: %d' % (filename, d_number))
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self.DescriptionOrder[f_number] = d
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self.images = sorted(self.DescriptionOrder.keys())
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self.Description = self.DescriptionOrder[self.images[0]]
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def direction_old(self):
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import numpy as np
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pos_a = np.array(map(float, self.DescriptionOrder[self.images[0]].get('image_position_patient').split('\\')))
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pos_z = np.array(map(float, self.DescriptionOrder[self.images[-1]].get('image_position_patient').split('\\')))
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# dir2 = pos_z - pos_a
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# print pos_a, pos_z, dir2
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# dir2 = dir2 / np.linalg.norm(dir2)
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# dir2 = [round(a) for a in dir2]
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image_orientation_patient = self.Description.get('image_orientation_patient').split('\\')
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image_position_patient = self.Description.get('image_position_patient').split('\\')
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dir = [round(float(a)) for a in image_orientation_patient]
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pos = map(float, image_position_patient)
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dir2 = (abs(np.array(dir[:3])+np.array(dir[3:]))-1)*(pos_a - pos_z)
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dir2 = dir2 / np.linalg.norm(dir2)
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print self.path
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print image_orientation_patient
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print image_position_patient
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print dir
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print dir2
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return dir + dir2.tolist()
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def direction_old2(self):
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import numpy as np
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# print self.DescriptionOrder[self.images[0]].get('image_number'), self.DescriptionOrder[self.images[0]].get('image_position_patient')
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# print self.DescriptionOrder[self.images[-1]].get('image_number'), self.DescriptionOrder[self.images[-1]].get('image_position_patient')
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pos_a = np.array(map(float, self.DescriptionOrder[self.images[0]].get('image_position_patient').split('\\')))
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pos_z = np.array(map(float, self.DescriptionOrder[self.images[-1]].get('image_position_patient').split('\\')))
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image_orientation_patient = self.Description.get('image_orientation_patient').split('\\')
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image_position_patient = self.Description.get('image_position_patient').split('\\')
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dir = [float(a) for a in image_orientation_patient]
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pos = map(float, image_position_patient)
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# dir2 = (pos_z - pos_a) * [1, -1, 1]/ (self.images[-1] - self.images[0])
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dir2 = (pos_z - pos_a) / (self.images[-1] - self.images[0])
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dir3 = np.array(dir+dir2.tolist())
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dir3 = dir3 / np.linalg.norm(dir3)
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print self.path
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print image_orientation_patient
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print pos_a, pos_z
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print self.images
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print dir
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print dir2
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print dir3
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return dir3.tolist()
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def direction(self):
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import numpy as np
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# print self.DescriptionOrder[self.images[0]].get('image_number'), self.DescriptionOrder[self.images[0]].get('image_position_patient')
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# print self.DescriptionOrder[self.images[-1]].get('image_number'), self.DescriptionOrder[self.images[-1]].get('image_position_patient')
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pos_a = np.array(map(float, self.DescriptionOrder[self.images[0]].get('image_position_patient').split('\\')))
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pos_z = np.array(map(float, self.DescriptionOrder[self.images[-1]].get('image_position_patient').split('\\')))
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image_orientation_patient = self.Description.get('image_orientation_patient').split('\\')
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image_position_patient = self.Description.get('image_position_patient').split('\\')
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dir = [round(float(a)) for a in image_orientation_patient]
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# dir = [float(a) for a in image_orientation_patient]
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pos = map(float, image_position_patient)
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# dir2 = (pos_z - pos_a) * [1, -1, 1]/ (self.images[-1] - self.images[0])
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dir2 = (pos_z - pos_a) / (self.images[-1] - self.images[0])
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dir2 = dir2 / np.linalg.norm(dir2)
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dir2 = [round(a) for a in dir2]
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# dir2 = [a for a in dir2]
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dir3 = np.array(dir+dir2)
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dir4 = np.linalg.inv(dir3.reshape(3,3))
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dir4 = np.transpose(dir3.reshape(3,3))
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print self.path
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print image_orientation_patient
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print pos_a, pos_z
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print self.images
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print dir
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print dir2
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print dir3
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print dir4
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print list(dir4.flat)
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return list(dir4.flat)
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# return dir3.tolist()
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def write(self, filename):
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import SimpleITK
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print self.Description.get('image_number')
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# print self.Description.get('referenced_image_sequence')
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# print self.Description.get('source_image_sequence')
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files = glob.glob("%s/*.jpg" % self.path)
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files.sort()
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sreader1 = SimpleITK.ImageSeriesReader()
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sreader1.SetFileNames(files)
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img = sreader1.Execute()
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pixel_spacing = self.Description.get('pixel_spacing').split('\\')
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try:
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slice_spacing = float(self.Description.get('slice_spacing'))
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except:
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slice_spacing = float(self.Description.get('slice_thickness'))
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img.SetDirection(self.direction())
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img.SetSpacing((float(pixel_spacing[0]), float(pixel_spacing[1]), slice_spacing))
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SimpleITK.WriteImage(img, filename)
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print img.GetDirection()
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print
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def get_description(self):
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return self.Description
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if __name__ == "__main__":
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series = IMPAX_Series('/shares/mnt/ntuh-cks/impax/2671292/20130417')
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series.write('/tmp/20130417.nii.gz')
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series = IMPAX_Series('/shares/mnt/ntuh-cks/impax/2671292/20130417C')
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series.write('/tmp/20130417C.nii.gz')
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# series = IMPAX_Series('/shares/mnt/ntuh-cks/impax/0397533/20120815')
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# series.write('/tmp/20120815.nii.gz')
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# d1 = series.get_description()
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#
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# series = IMPAX_Series('/shares/mnt/ntuh-cks/impax/0397533/20120815C')
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# series.write('/tmp/20120815C.nii.gz')
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#
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# series = IMPAX_Series('/shares/mnt/ntuh-cks/impax/0397533/20160216')
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# series.write('/tmp/20160216.nii.gz')
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#
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# series = IMPAX_Series('/shares/mnt/ntuh-cks/impax/0397533/20160216C')
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# series.write('/tmp/20160216C.nii.gz')
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# d2 = series.get_description()
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#
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# import pprint
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# pp = pprint.PrettyPrinter(indent=4)
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# print d1-d2
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# pp.pprint(d1-d2)
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