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Update PDF slice visualization #12

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Update PDF slice visualization #12

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78a5da4
modify visualization offsets to be based dwi slice number
praitayini Jun 4, 2023
52339d9
fix offset variable
praitayini Jun 5, 2023
f4cf87a
fix offset syntax error
praitayini Jun 6, 2023
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14 changes: 12 additions & 2 deletions src/CODE/dtiQA_v7/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -750,7 +750,7 @@ def pescheme2axis(pe_axis, pe_dir, aff):

# Function Definitions: Visualization

def slice_nii(nii_file, offsets=[0], custom_aff=[], min_percentile=0, max_percentile=100, min_intensity=np.nan, max_intensity=np.nan, det=False):
def slice_nii(nii_file, offsets=False, custom_aff=[], min_percentile=0, max_percentile=100, min_intensity=np.nan, max_intensity=np.nan, det=False):

if det:
img, aff, hdr = load_nii(nii_file, ndim=4)
Expand Down Expand Up @@ -782,10 +782,20 @@ def slice_nii(nii_file, offsets=[0], custom_aff=[], min_percentile=0, max_percen
i1 = int(round(img.shape[1] / 2, 1))
i2 = int(round(img.shape[2] / 2, 1))

if offsets:
slice1 = int(round(i2 * 0.3, 1))
slice2 = int(round(i2 * 0.4, 1))
slice3 = int(round(i2 * 0.5, 1))
slice4 = int(round(i2 * 0.6, 1))
slice5 = int(round(i2 * 0.7, 1))
offset_value = [ slice1, slice2, slice3, slice4, slice5 ]
else:
offset_value = [0]

i0s = []
i1s = []
i2s = []
for offset in offsets:
for offset in offset_value:
i0s.append(i0 + offset)
i1s.append(i1 + offset)
i2s.append(i2 + offset)
Expand Down
6 changes: 3 additions & 3 deletions src/CODE/dtiQA_v7/vis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -581,7 +581,7 @@ def vis_degibbs(dwi_files, bvals_files, dwi_degibbs_files, gains, vis_dir):

# Plot 5 central triplanar views

res_slices, res_vox_dim, res_min, res_max = utils.slice_nii(res_file, offsets=[-10, -5, 0, 5, 10], min_intensity=0, max_percentile=99)
res_slices, res_vox_dim, res_min, res_max = utils.slice_nii(res_file, offsets=True, min_intensity=0, max_percentile=99)
temp_vis_file = _vis_vol(res_slices, res_vox_dim, res_min, res_max, temp_dir, name='Gibbs_Deringing,_Averaged_Residuals_of_b_=_0_Volumes', comment='Residuals should be larger at high-contrast interfaces', colorbar=False)
degibbs_vis_file = utils.rename_file(temp_vis_file, os.path.join(vis_dir, 'degibbs.pdf'))

Expand Down Expand Up @@ -949,7 +949,7 @@ def vis_dwi(dwi_file, bvals_shelled, bvecs_file, cnr_dict, vis_dir):
bX = bvals[i]
bXs_file, num_bXs, _ = utils.dwi_extract(dwi_file, bvals_shelled_file, temp_dir, target_bval=bX, first_only=False)
bXs_avg_file = utils.dwi_avg(bXs_file, temp_dir)
bXs_avg_slices, bXs_avg_vox_dim, bXs_avg_min, bXs_avg_max = utils.slice_nii(bXs_avg_file, offsets=[-10, -5, 0, 5, 10], min_intensity=0, max_percentile=SHARED_VARS.VIS_PERCENTILE_MAX)
bXs_avg_slices, bXs_avg_vox_dim, bXs_avg_min, bXs_avg_max = utils.slice_nii(bXs_avg_file, offsets=True, min_intensity=0, max_percentile=SHARED_VARS.VIS_PERCENTILE_MAX)

cnr = '{:.3f}'.format(cnr_dict[bX])
cnr_label = 'SNR' if bX == 0 else 'CNR'
Expand All @@ -974,7 +974,7 @@ def vis_scalar(scalar_file, vis_dir, name='?', comment=''):
elif name == 'MD':
scalar_max = SHARED_VARS.ADC_WATER

scalar_slices, scalar_vox_dim, _, _ = utils.slice_nii(scalar_file, offsets=[-10, -5, 0, 5, 10])
scalar_slices, scalar_vox_dim, _, _ = utils.slice_nii(scalar_file, offsets=True)
scalar_vis_file = _vis_vol(scalar_slices, scalar_vox_dim, scalar_min, scalar_max, vis_dir, name=name, comment=comment, colorbar=True)

return scalar_vis_file
Expand Down