use external (py)dcm2niix package

[casperdcl]

• replace run([resources.DCM2NIIX, ...]) with dicom2nifti.convert_directory
  • automatically creates the output filename (based on DICOM header SeriesDescription
  • ensure imio.dcm2nii supports fimout/fprefix/fcomment
    • dicom2nifti.convert_directory doesn't output file name(s) output files from convert_dir icometrix/dicom2nifti#107
    • keep supporting old version via option flag
    • check dynamic rescaling slope, units (Bq?), etc...
• move dcm2niix to separate package #23
  • pip pkg rordenlab/dcm2niix#573

outdated test script

from pathlib import Path
from subprocess import check_output
from time import time

import dicom2nifti
from miutil import imio, plot
from niftypet.nimpa import resources as rs

dir_in = './umap'
#dcm2niix = str(Path("~/NiftyPET_tools/dcm2niix/bin/dcm2niix").expanduser())
dcm2niix = rs.DCM2NIIX

def clean_dir(pth):
    if pth.is_dir():
        [i.unlink() for i in pth.glob('*.*')]
        pth.rmdir()
    pth.mkdir()
    return str(pth)

dir_out = clean_dir(Path(dir_in + '-dcm2niix'))
tic = time()
check_output([dcm2niix, '-f', 'test', '-o', dir_out, dir_in])
print(f"{time()-tic:.3f} elapsed (dcm2niix)")

dir_out = clean_dir(Path(dir_in + '-dicom2nifti'))
tic = time()
dicom2nifti.convert_directory(dir_in, dir_out)
print(f"{time()-tic:.3f} elapsed (dicom2nifti)")

pth_in = Path(dir_in)
plot.imscroll({i: imio.imread(i) for i in pth_in.parent.glob(pth_in.stem + '-*/*.nii*')})
plot.show()

caveat: it's ~5x slower than dcm2niix (icometrix/dicom2nifti#102)

---

• fixes move dcm2niix to separate package #23

[codecov]

Codecov Report

Merging #24 (70da069) into devel (7099d6e) will decrease coverage by 0.04%.
The diff coverage is 3.33%.

@@           Coverage Diff            @@
##           devel     #24      +/-   ##
========================================
- Coverage   9.56%   9.52%   -0.05%     
========================================
  Files          9       9              
  Lines       2059    2047      -12     
========================================
- Hits         197     195       -2     
+ Misses      1862    1852      -10     

Impacted Files	Coverage Δ
niftypet/nimpa/prc/imio.py	5.33% <0.00%> (-0.10%)	⬇️
niftypet/nimpa/prc/prc.py	5.66% <25.00%> (-0.12%)	⬇️

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