OverflowError: Python integer -1024 out of bounds for uint16 #150
Description
Hi, I am getting this overflow error when converting my image from DICOM to NIFTI. I had quick look through your code, I think one of your conditions for converting to float must be missing when doing the scaling. Let me know if you can fix this.
OverflowError Traceback (most recent call last)
Cell In[2], line 4
2 dicom_path = Path("data/practical1/CT-PET-VI-02/CT_for_PET/")
3 output_path = Path("data/practical1/ct_for_pet.nii.gz")
----> 4 dicom2nifti.dicom_series_to_nifti(dicom_path, output_path, reorient_nifti=False)
File c:\Users\clead\anaconda3\envs\dicom2nifti\Lib\site-packages\dicom2nifti\convert_dicom.py:79, in dicom_series_to_nifti(original_dicom_directory, output_file, reorient_nifti)
75 shutil.copytree(original_dicom_directory, dicom_directory)
77 dicom_input = common.read_dicom_directory(dicom_directory)
---> 79 return dicom_array_to_nifti(dicom_input, output_file, reorient_nifti)
81 except AttributeError as exception:
82 raise exception
File c:\Users\clead\anaconda3\envs\dicom2nifti\Lib\site-packages\dicom2nifti\convert_dicom.py:119, in dicom_array_to_nifti(dicom_list, output_file, reorient_nifti)
116 vendor = _get_vendor(dicom_list)
118 if vendor == Vendor.GENERIC:
--> 119 results = convert_generic.dicom_to_nifti(dicom_list, output_file)
120 elif vendor == Vendor.SIEMENS:
121 results = convert_siemens.dicom_to_nifti(dicom_list, output_file)
File c:\Users\clead\anaconda3\envs\dicom2nifti\Lib\site-packages\dicom2nifti\convert_generic.py:274, in dicom_to_nifti(dicom_input, output_file)
270 nii_image, max_slice_increment = _convert_slice_incement_inconsistencies(dicom_input)
271 # do the normal conversion
272 else:
273 # Get data; originally z,y,x, transposed to x,y,z
--> 274 data = common.get_volume_pixeldata(dicom_input)
276 affine, max_slice_increment = common.create_affine(dicom_input)
278 # Convert to nifti
File c:\Users\clead\anaconda3\envs\dicom2nifti\Lib\site-packages\dicom2nifti\common.py:313, in get_volume_pixeldata(sorted_slices)
310 for i, slice_ in enumerate(sorted_slices):
311 # create copy so we don't load all pixel data on the original slice that is kept in memory
312 slice_copy = copy.deepcopy(slice_)
--> 313 slice_data = _get_slice_pixeldata(slice_copy)
314 del slice_copy
315 if combined_dtype is None:
File c:\Users\clead\anaconda3\envs\dicom2nifti\Lib\site-packages\dicom2nifti\common.py:355, in _get_slice_pixeldata(dicom_slice)
353 data[data > max_value] = numpy.bitwise_or(data[data > max_value], invert_value)
354 pass
--> 355 return apply_scaling(data, dicom_slice)
File c:\Users\clead\anaconda3\envs\dicom2nifti\Lib\site-packages\dicom2nifti\common.py:509, in apply_scaling(data, dicom_headers)
500 rescale_intercept = dicom_headers.RescaleIntercept
501 # try:
502 # # this section can sometimes fail due to unknown private fields
503 # if private_scale_slope_tag in dicom_headers:
(...)
507 # except:
508 # pass
--> 509 return do_scaling(data, rescale_slope, rescale_intercept)
510 else:
511 return data
File c:\Users\clead\anaconda3\envs\dicom2nifti\Lib\site-packages\dicom2nifti\common.py:540, in do_scaling(data, rescale_slope, rescale_intercept, private_scale_slope, private_scale_intercept)
537 else:
538 # Determine required range
539 minimum_required, maximum_required = data.min(), data.max()
--> 540 minimum_required = min([minimum_required, minimum_required * rescale_slope + rescale_intercept,
541 maximum_required * rescale_slope + rescale_intercept])
542 maximum_required = max([maximum_required, minimum_required * rescale_slope + rescale_intercept,
543 maximum_required * rescale_slope + rescale_intercept])
545 # Determine required datatype from that
OverflowError: Python integer -1024 out of bounds for uint16