ImageProcessingBackend/Formatcov.py at main · Hi5App/ImageProcessingBackend · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126

"""
Load and save v3draw stack files that are supported by V3D
by Lei Qu
20200330
"""
import SimpleITK as sitk
import numpy as np
import struct
import os


def load_v3d_raw_img_file1(filename):
    im = {}

    f_obj = open(filename, 'rb')

    # read image header - formatkey(24bytes)
    len_formatkey = len('raw_image_stack_by_hpeng')
    formatkey = f_obj.read(len_formatkey)
    formatkey = struct.unpack(str(len_formatkey) + 's', formatkey)
    if formatkey[0] != b'raw_image_stack_by_hpeng':
        print("ERROR: File unrecognized (not raw, v3draw) or corrupted.")
        f_obj.close()
        return im

    # read image header - endianCode(1byte)
    endiancode = f_obj.read(1)
    endiancode = struct.unpack('c', endiancode)  # 'c' = char
    endiancode = endiancode[0]
    if endiancode != b'B' and endiancode != b'L':
        print("ERROR: Only supports big- or little- endian,"
              " but not other format. Check your data endian.")
        f_obj.close()
        return im

    # read image header - datatype(2bytes)
    datatype = f_obj.read(2)
    if endiancode == b'L':
        datatype = struct.unpack('<h', datatype)  # 'h' = short
    else:
        datatype = struct.unpack('>h', datatype)  # 'h' = short
    datatype = datatype[0]
    if datatype < 1 or datatype > 4:
        print("ERROR: Unrecognized data type code [%d]. "
              "The file type is incorrect or this code is not supported." % (datatype))
        f_obj.close()
        return im

    # read image header - size(4*4bytes)
    size = f_obj.read(4 * 4)
    if endiancode == b'L':
        size = struct.unpack('<4l', size)  # 'l' = long
    else:
        size = struct.unpack('>4l', size)  # 'l' = long
    # print(size)

    # read image data
    npixels = size[0] * size[1] * size[2] * size[3]
    im_data = f_obj.read()
    if datatype == 1:
        im_data = np.frombuffer(im_data, np.uint8)
    elif datatype == 2:
        im_data = np.frombuffer(im_data, np.uint16)
    else:
        im_data = np.frombuffer(im_data, np.float32)
    if len(im_data) != npixels:
        print("ERROR: Read image data size != image size. Check your data.")
        return im

    im_data = im_data.reshape((size[3], size[2], size[1], size[0]))
    # print(im_data.shape)
    # print(im_data.shape)
    im_data = np.moveaxis(im_data, 0, -1)
    # print(im_data.shape)
    im_data = np.moveaxis(im_data, 0, -2)
    # print(im_data.shape)
    f_obj.close()

    im['endian'] = endiancode
    im['datatype'] = datatype
    im['size'] = im_data.shape
    im['data'] = im_data

    return im


def save_v3d_raw_img_file1(im, filename):
    if filename[-4:] != '.raw' and filename[-7:] != '.v3draw':
        print("ERROR: Unsupportted file format. return!")


    f_obj = open(filename, 'wb')

    # write image header - formatkey(24bytes)
    formatkey = b'raw_image_stack_by_hpeng'
    formatkey = struct.pack('<24s', formatkey)
    f_obj.write(formatkey)

    # write image header - endianCode(1byte)
    endiancode = b'L'
    endiancode = struct.pack('<s', endiancode)
    f_obj.write(endiancode)

    # write image header - datatype(2bytes)
    datatype = im['datatype']
    datatype = struct.pack('<h', datatype)  # 'h' = short
    f_obj.write(datatype)

    # write image header - size(4*4bytes)
    size = im['size']
    size = struct.pack('<4l', size[1], size[0], size[2], size[3])  # 'l' = long
    f_obj.write(size)

    # write image data
    im_data = im['data']

    im_data = np.moveaxis(im_data, -2, 0)
    im_data = np.moveaxis(im_data, -1, 0)
    # print(im_data.shape)
    im_data = im_data.tobytes()
    f_obj.write(im_data)
    f_obj.close()