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I would like to create two pydicom file from one. But I can't save file in *.dcm format with annotations.

import pydicom
from pydicom.data import get_testdata_files
# read the dicom file
ds = pydicom.dcmread(test_image_fps[0])
# find the shape of your pixel data
shape = ds.pixel_array.shape
# get the half of the x dimension. For the y dimension use shape[0]
half_x = int(shape[1] / 2)
# slice the halves
# [first_axis, second_axis] so [:,:half_x] means slice all from first axis, slice 0 to half_x from second axis
data = ds.pixel_array[:, :half_x]
print('The image has x '.format(data.shape[0],
 data.shape[1]))

# print the image information given in the dataset
print(data)
data.save_as("/my/path/after.dcm")

'numpy.ndarray' object has no attribute 'save_as

python pydicom

share|improve this question

edited Mar 26 at 0:45

Badum

asked Mar 25 at 23:38

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add a comment | 

0

0

I would like to create two pydicom file from one. But I can't save file in *.dcm format with annotations.

import pydicom
from pydicom.data import get_testdata_files
# read the dicom file
ds = pydicom.dcmread(test_image_fps[0])
# find the shape of your pixel data
shape = ds.pixel_array.shape
# get the half of the x dimension. For the y dimension use shape[0]
half_x = int(shape[1] / 2)
# slice the halves
# [first_axis, second_axis] so [:,:half_x] means slice all from first axis, slice 0 to half_x from second axis
data = ds.pixel_array[:, :half_x]
print('The image has x '.format(data.shape[0],
 data.shape[1]))

# print the image information given in the dataset
print(data)
data.save_as("/my/path/after.dcm")

'numpy.ndarray' object has no attribute 'save_as

python pydicom

share|improve this question

edited Mar 26 at 0:45

Badum

asked Mar 25 at 23:38

BadumBadum

4077 bronze badges

add a comment | 

I would like to create two pydicom file from one. But I can't save file in *.dcm format with annotations.

import pydicom
from pydicom.data import get_testdata_files
# read the dicom file
ds = pydicom.dcmread(test_image_fps[0])
# find the shape of your pixel data
shape = ds.pixel_array.shape
# get the half of the x dimension. For the y dimension use shape[0]
half_x = int(shape[1] / 2)
# slice the halves
# [first_axis, second_axis] so [:,:half_x] means slice all from first axis, slice 0 to half_x from second axis
data = ds.pixel_array[:, :half_x]
print('The image has x '.format(data.shape[0],
 data.shape[1]))

# print the image information given in the dataset
print(data)
data.save_as("/my/path/after.dcm")

'numpy.ndarray' object has no attribute 'save_as

python pydicom

share|improve this question

edited Mar 26 at 0:45

Badum

asked Mar 25 at 23:38

BadumBadum

4077 bronze badges

import pydicom
from pydicom.data import get_testdata_files
# read the dicom file
ds = pydicom.dcmread(test_image_fps[0])
# find the shape of your pixel data
shape = ds.pixel_array.shape
# get the half of the x dimension. For the y dimension use shape[0]
half_x = int(shape[1] / 2)
# slice the halves
# [first_axis, second_axis] so [:,:half_x] means slice all from first axis, slice 0 to half_x from second axis
data = ds.pixel_array[:, :half_x]
print('The image has x '.format(data.shape[0],
 data.shape[1]))

# print the image information given in the dataset
print(data)
data.save_as("/my/path/after.dcm")

'numpy.ndarray' object has no attribute 'save_as

share|improve this question

edited Mar 26 at 0:45

Badum

asked Mar 25 at 23:38

BadumBadum

4077 bronze badges

share|improve this question

edited Mar 26 at 0:45

Badum

asked Mar 25 at 23:38

BadumBadum

4077 bronze badges

asked Mar 25 at 23:38

BadumBadum

4077 bronze badges

asked Mar 25 at 23:38

BadumBadum

4077 bronze badges

1 Answer
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Info on this can be foud in the pydicom documentation.

Remark on "your" ;) code: data = ds.pixel_array[:, :half_x] assigns a view of the numpy.ndarray that is ds.pixel_array to data. Calling data.save_as() expectedly fails because that is an attribute of ds not data. As per the documentation you need to write to the ds.PixelData attribute like so:

ds.PixelData = data.tobytes() # where data is a numpy.ndarray or a view of an numpy.ndarray

# if the shape of your pixel data changes ds.Rows and ds.Columns must be updated,
# otherwise calls to ds.pixel_array.shape will fail
ds.Rows = 512 # update with correct number of rows
ds.Columns = 512 # update with the correct number of columns
ds.save_as("/my/path/after.dcm") 

share|improve this answer

answered Mar 27 at 12:56

g_uintg_uint

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Info on this can be foud in the pydicom documentation.

Remark on "your" ;) code: data = ds.pixel_array[:, :half_x] assigns a view of the numpy.ndarray that is ds.pixel_array to data. Calling data.save_as() expectedly fails because that is an attribute of ds not data. As per the documentation you need to write to the ds.PixelData attribute like so:

ds.PixelData = data.tobytes() # where data is a numpy.ndarray or a view of an numpy.ndarray

# if the shape of your pixel data changes ds.Rows and ds.Columns must be updated,
# otherwise calls to ds.pixel_array.shape will fail
ds.Rows = 512 # update with correct number of rows
ds.Columns = 512 # update with the correct number of columns
ds.save_as("/my/path/after.dcm") 

share|improve this answer

answered Mar 27 at 12:56

g_uintg_uint

9761111 silver badges2424 bronze badges

add a comment | 

0

Info on this can be foud in the pydicom documentation.

Remark on "your" ;) code: data = ds.pixel_array[:, :half_x] assigns a view of the numpy.ndarray that is ds.pixel_array to data. Calling data.save_as() expectedly fails because that is an attribute of ds not data. As per the documentation you need to write to the ds.PixelData attribute like so:

ds.PixelData = data.tobytes() # where data is a numpy.ndarray or a view of an numpy.ndarray

# if the shape of your pixel data changes ds.Rows and ds.Columns must be updated,
# otherwise calls to ds.pixel_array.shape will fail
ds.Rows = 512 # update with correct number of rows
ds.Columns = 512 # update with the correct number of columns
ds.save_as("/my/path/after.dcm") 

share|improve this answer

answered Mar 27 at 12:56

g_uintg_uint

9761111 silver badges2424 bronze badges

add a comment | 

Info on this can be foud in the pydicom documentation.

Remark on "your" ;) code: data = ds.pixel_array[:, :half_x] assigns a view of the numpy.ndarray that is ds.pixel_array to data. Calling data.save_as() expectedly fails because that is an attribute of ds not data. As per the documentation you need to write to the ds.PixelData attribute like so:

ds.PixelData = data.tobytes() # where data is a numpy.ndarray or a view of an numpy.ndarray

# if the shape of your pixel data changes ds.Rows and ds.Columns must be updated,
# otherwise calls to ds.pixel_array.shape will fail
ds.Rows = 512 # update with correct number of rows
ds.Columns = 512 # update with the correct number of columns
ds.save_as("/my/path/after.dcm") 

share|improve this answer

answered Mar 27 at 12:56

g_uintg_uint

9761111 silver badges2424 bronze badges

ds.PixelData = data.tobytes() # where data is a numpy.ndarray or a view of an numpy.ndarray

# if the shape of your pixel data changes ds.Rows and ds.Columns must be updated,
# otherwise calls to ds.pixel_array.shape will fail
ds.Rows = 512 # update with correct number of rows
ds.Columns = 512 # update with the correct number of columns
ds.save_as("/my/path/after.dcm") 

share|improve this answer

answered Mar 27 at 12:56

g_uintg_uint

9761111 silver badges2424 bronze badges

answered Mar 27 at 12:56

g_uintg_uint

9761111 silver badges2424 bronze badges

answered Mar 27 at 12:56

g_uintg_uint

9761111 silver badges2424 bronze badges