Image3dAPI/TestPython/TestPython.py at master · SteveKauffman/Image3dAPI · 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
## Sample code to demonstrate how to access Image3dAPI from a python script
import platform
import comtypes
import comtypes.client
import numpy as np


def SafeArrayToNumpy (safearr_ptr, copy=True):
    """Convert a SAFEARRAY buffer to its numpy equivalent"""
    import ctypes

    # only support 1D data for now
    assert(comtypes._safearray.SafeArrayGetDim(safearr_ptr) == 1)

    # access underlying pointer
    data_ptr = ctypes.POINTER(safearr_ptr._itemtype_)()
    comtypes._safearray.SafeArrayAccessData(safearr_ptr, ctypes.byref(data_ptr))

    upper_bound = comtypes._safearray.SafeArrayGetUBound(safearr_ptr, 1) + 1 # +1 to go from inclusive to exclusive bound
    lower_bound = comtypes._safearray.SafeArrayGetLBound(safearr_ptr, 1)
    array_size = upper_bound - lower_bound

    # wrap pointer in numpy array
    arr = np.ctypeslib.as_array(data_ptr,shape=(array_size,))
    return np.copy(arr) if copy else arr


def FrameTo3dArray (frame):
    """Convert Image3d data into a numpy 3D array"""
    arr_1d = SafeArrayToNumpy(frame.data, copy=False)
    assert(arr_1d.dtype == np.uint8) # only tested with 1byte/elm

    arr_3d = np.lib.stride_tricks.as_strided(arr_1d, shape=frame.dims, strides=(1, frame.stride0, frame.stride1))
    return np.copy(arr_3d)


if __name__=="__main__":
    # load type library
    if "32" in platform.architecture()[0]:
        Image3dAPI = comtypes.client.GetModule("../Win32/Image3dAPI.tlb")
    else:
        Image3dAPI = comtypes.client.GetModule("../x64/Image3dAPI.tlb")

    # create loader object
    loader = comtypes.client.CreateObject("DummyLoader.Image3dFileLoader")
    loader = loader.QueryInterface(Image3dAPI.IImage3dFileLoader)

    # load file
    err_type, err_msg = loader.LoadFile("dummy.dcm")
    source = loader.GetImageSource()

    # retrieve probe info
    probe = source.GetProbeInfo()
    print("Probe name: "+probe.name)
    print("Probe type: "+str(probe.type))

    # retrieve ECG info
    ecg = source.GetECG()
    print("ECG start: "+str(ecg.start_time))
    print("ECG delta: "+str(ecg.delta_time))
    samples = SafeArrayToNumpy(ecg.samples)
    trig_times = SafeArrayToNumpy(ecg.trig_times)

    # get bounding box
    bbox = source.GetBoundingBox()
    origin = [bbox.origin_x, bbox.origin_y, bbox.origin_z]
    dir1   = [bbox.dir1_x,   bbox.dir1_y,   bbox.dir1_z]
    dir2   = [bbox.dir2_x,   bbox.dir2_y,   bbox.dir2_z]
    dir3   = [bbox.dir3_x,   bbox.dir3_y,   bbox.dir3_z]

    color_map = source.GetColorMap()

    frame_count = source.GetFrameCount()
    for i in range(frame_count):
        max_res = np.ctypeslib.as_ctypes(np.array([64, 64, 64], dtype=np.ushort))
        frame = source.GetFrame(i, bbox, max_res)

        print("Frame metadata:")
        print("  time:   "+str(frame.time))
        print("  format: "+str(frame.format))
        print("  dims:  ("+str(frame.dims[0])+", "+str(frame.dims[1])+", "+str(frame.dims[2])+")")

        data = FrameTo3dArray(frame)
        print("  shape: "+str(data.shape))