In [29]:
%pylab inline
import os.path as op
import io3d
import sed3
In [25]:
output_path="e:data/medical/processed/porcine_liver_ct/"
In [52]:
pths = [
[r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\MakroCT\HEAD_01_HEADROUTINE_(ADULT)_20130218_133846_968000\HEAD_5_0_H31S_0004", "P01_MakroCT_HEAD_5_0_H31S_0004.mhd"],
[r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\MakroCT_po_rozrezani\HEAD_0_6_H20S_0003", "P01_MakroCT_po_rozrezani_HEAD_0_6_H20S_0003.mhd"],
[r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\MikroCT-nejhrubsi_rozliseni\DICOM_liver-1st-important_Macro_pixel-size53.0585um", "P01_a_MikroCT-nejhrubsi_rozliseni_DICOM_liver-1st-important_Macro_pixel-size53.0585um.mhd"],
# [r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\MikroCT-stredne_podrobne\Zdrojove_obrazky\Part1-130624_jatra2x1xX-A_1x_DICOM", "P01_a_MikroCT-stredne_podrobne_Part1-130624_jatra2x1xX-A_1x_DICOM.mhd"],
# [r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-a\Nejlep_rozl_vycistene\130624_jatra2x1xX-A_4x_DICOM_bestRECON-8bit_binning1", "P01_a_Nejlep_rozl_vycistene_130624_jatra2x1xX-A_4x_DICOM_bestRECON-8bit_binning1.mhd"],
[r"E:\data\medical\orig\ct_porcine_liver\P01\29-8-12-b\Prase_1_druhe_vys", "P01_b_Prase_1_druhe_vys.mhd", 6],
[r"E:\data\medical\orig\ct_porcine_liver\P01\c\DICOM-8bit-lowres_130926_liver-29-8-12-C_4x", "P01_c_DICOM-8bit-lowres_130926_liver-29-8-12-C_4x.mhd"],
[r"E:\data\medical\orig\ct_porcine_liver\P01\c\DICOM-8bit-lowres_130926_liver-29-8-12-C_1x", "P01_c_DICOM-8bit-lowres_130926_liver-29-8-12-C_1x.mhd"],
[r"E:\data\medical\orig\ct_porcine_liver\P01\c\DICOM-8bit_130926_liver-29-8-12-C_1x", "P01_c_DICOM-8bit_130926_liver-29-8-12-C_1x.mhd"],
[r"E:\data\medical\orig\ct_porcine_liver\P01\29_8_12_d\DICOM-8bit-lowres_130926_liver-29-8-12-D_4x", "P01_d_DICOM-8bit-lowres_130926_liver-29-8-12-D_4x.mhd"],
[r"E:\data\medical\orig\ct_porcine_liver\P12_P12\PRIVATE_00_KOROZIVNI_PREPARAT_(ADULT)_20151108_173623_929000\ABDOMENNATIVE_0_6_I26F_3_0005", "P12_ABDOMENNATIVE_0_6_I26F_3_0005.mhd"],
[r"E:\data\medical\orig\ct_porcine_liver\P12_P12\Nejvyssi_rozliseni_DICOM_160222_P-12-1_4x", "P12_Nejvyssi_rozliseni_DICOM_160222_P-12-1_4x.mhd"]
]
In [53]:
for fns in pths[:]:
if len(fns) > 2:
series_number = fns[2]
else:
series_number = None
datap = io3d.read(fns[0], series_number=series_number)
plt.figure(figsize=(10, 6))
plt.suptitle(fns[1])
slice_step = int(datap["data3d"].shape[0] / 5)
sed3.show_slices(datap["data3d"], slice_step=slice_step)
io3d.write(datap, op.join(output_path, fns[1]))