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Reference Manual 20230220
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@alexdaniel654
alexdaniel654 committed Feb 20, 2023
1 parent 73e910e commit 391ac92
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Showing 17 changed files with 193 additions and 53 deletions.
6 changes: 3 additions & 3 deletions mapping/b0.html
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,7 @@ <h1 class="title">Module <code>ukat.mapping.b0</code></h1>
b0_nifti = nib.Nifti1Image(self.b0_map, affine=self.affine)
nib.save(b0_nifti, base_path + &#39;_b0_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
elif result == &#39;phase0&#39;:
Expand Down Expand Up @@ -404,7 +404,7 @@ <h2 id="parameters">Parameters</h2>
b0_nifti = nib.Nifti1Image(self.b0_map, affine=self.affine)
nib.save(b0_nifti, base_path + &#39;_b0_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
elif result == &#39;phase0&#39;:
Expand Down Expand Up @@ -477,7 +477,7 @@ <h2 id="parameters">Parameters</h2>
b0_nifti = nib.Nifti1Image(self.b0_map, affine=self.affine)
nib.save(b0_nifti, base_path + &#39;_b0_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
elif result == &#39;phase0&#39;:
Expand Down
12 changes: 6 additions & 6 deletions mapping/diffusion.html
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Original file line number Diff line number Diff line change
Expand Up @@ -284,7 +284,7 @@ <h1 class="title">Module <code>ukat.mapping.diffusion</code></h1>
affine=self.affine)
nib.save(adc_err_nifti, base_path + &#39;_adc_err.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -435,7 +435,7 @@ <h1 class="title">Module <code>ukat.mapping.diffusion</code></h1>
nib.save(color_fa_nifti, base_path +
&#39;_color_fa_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -811,7 +811,7 @@ <h2 id="parameters">Parameters</h2>
affine=self.affine)
nib.save(adc_err_nifti, base_path + &#39;_adc_err.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -870,7 +870,7 @@ <h2 id="parameters">Parameters</h2>
affine=self.affine)
nib.save(adc_err_nifti, base_path + &#39;_adc_err.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -1097,7 +1097,7 @@ <h2 id="parameters">Parameters</h2>
nib.save(color_fa_nifti, base_path +
&#39;_color_fa_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -1160,7 +1160,7 @@ <h2 id="parameters">Parameters</h2>
nib.save(color_fa_nifti, base_path +
&#39;_color_fa_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down
49 changes: 29 additions & 20 deletions mapping/mtr.html
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Original file line number Diff line number Diff line change
Expand Up @@ -92,12 +92,12 @@ <h1 class="title">Module <code>ukat.mapping.mtr</code></h1>
else:
self.mask = mask
# The assumption is that MT_OFF comes first in `pixel_array`
self.mt_off = self.pixel_array[..., 0] * self.mask
self.mt_off = np.squeeze(self.pixel_array[..., 0] * self.mask)
# The assumption is that MT_ON comes second in `pixel_array`
self.mt_on = self.pixel_array[..., 1] * self.mask
self.mt_on = np.squeeze(self.pixel_array[..., 1] * self.mask)
# Magnetisation Transfer Ratio calculation
self.mtr_map = np.nan_to_num(((self.mt_off - self.mt_on) /
self.mt_off), posinf=0, neginf=0)
self.mtr_map = np.squeeze(np.nan_to_num(((self.mt_off - self.mt_on) /
self.mt_off), posinf=0, neginf=0))

def to_nifti(self, output_directory=os.getcwd(), base_file_name=&#39;Output&#39;,
maps=&#39;all&#39;):
Expand All @@ -122,18 +122,21 @@ <h1 class="title">Module <code>ukat.mapping.mtr</code></h1>
for result in maps:
if result == &#39;mtr&#39; or result == &#39;mtr_map&#39;:
mtr_nifti = nib.Nifti1Image(self.mtr_map,
affine=self.affine)
affine=self.affine,
dtype=float)
nib.save(mtr_nifti, base_path + &#39;_mtr_map.nii.gz&#39;)
elif result == &#39;mt_on&#39;:
mt_on_nifti = nib.Nifti1Image(self.mt_on,
affine=self.affine)
affine=self.affine,
dtype=float)
nib.save(mt_on_nifti, base_path + &#39;_mt_on.nii.gz&#39;)
elif result == &#39;mt_off&#39;:
mt_off_nifti = nib.Nifti1Image(self.mt_off,
affine=self.affine)
affine=self.affine,
dtype=float)
nib.save(mt_off_nifti, base_path + &#39;_mt_off.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -256,12 +259,12 @@ <h2 id="parameters">Parameters</h2>
else:
self.mask = mask
# The assumption is that MT_OFF comes first in `pixel_array`
self.mt_off = self.pixel_array[..., 0] * self.mask
self.mt_off = np.squeeze(self.pixel_array[..., 0] * self.mask)
# The assumption is that MT_ON comes second in `pixel_array`
self.mt_on = self.pixel_array[..., 1] * self.mask
self.mt_on = np.squeeze(self.pixel_array[..., 1] * self.mask)
# Magnetisation Transfer Ratio calculation
self.mtr_map = np.nan_to_num(((self.mt_off - self.mt_on) /
self.mt_off), posinf=0, neginf=0)
self.mtr_map = np.squeeze(np.nan_to_num(((self.mt_off - self.mt_on) /
self.mt_off), posinf=0, neginf=0))

def to_nifti(self, output_directory=os.getcwd(), base_file_name=&#39;Output&#39;,
maps=&#39;all&#39;):
Expand All @@ -286,18 +289,21 @@ <h2 id="parameters">Parameters</h2>
for result in maps:
if result == &#39;mtr&#39; or result == &#39;mtr_map&#39;:
mtr_nifti = nib.Nifti1Image(self.mtr_map,
affine=self.affine)
affine=self.affine,
dtype=float)
nib.save(mtr_nifti, base_path + &#39;_mtr_map.nii.gz&#39;)
elif result == &#39;mt_on&#39;:
mt_on_nifti = nib.Nifti1Image(self.mt_on,
affine=self.affine)
affine=self.affine,
dtype=float)
nib.save(mt_on_nifti, base_path + &#39;_mt_on.nii.gz&#39;)
elif result == &#39;mt_off&#39;:
mt_off_nifti = nib.Nifti1Image(self.mt_off,
affine=self.affine)
affine=self.affine,
dtype=float)
nib.save(mt_off_nifti, base_path + &#39;_mt_off.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -352,18 +358,21 @@ <h2 id="parameters">Parameters</h2>
for result in maps:
if result == &#39;mtr&#39; or result == &#39;mtr_map&#39;:
mtr_nifti = nib.Nifti1Image(self.mtr_map,
affine=self.affine)
affine=self.affine,
dtype=float)
nib.save(mtr_nifti, base_path + &#39;_mtr_map.nii.gz&#39;)
elif result == &#39;mt_on&#39;:
mt_on_nifti = nib.Nifti1Image(self.mt_on,
affine=self.affine)
affine=self.affine,
dtype=float)
nib.save(mt_on_nifti, base_path + &#39;_mt_on.nii.gz&#39;)
elif result == &#39;mt_off&#39;:
mt_off_nifti = nib.Nifti1Image(self.mt_off,
affine=self.affine)
affine=self.affine,
dtype=float)
nib.save(mt_off_nifti, base_path + &#39;_mt_off.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down
6 changes: 3 additions & 3 deletions mapping/t1.html
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Original file line number Diff line number Diff line change
Expand Up @@ -372,7 +372,7 @@ <h1 class="title">Module <code>ukat.mapping.t1</code></h1>
affine=self.affine)
nib.save(r1_nifti, base_path + &#39;_r1_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -1205,7 +1205,7 @@ <h2 id="parameters">Parameters</h2>
affine=self.affine)
nib.save(r1_nifti, base_path + &#39;_r1_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -1326,7 +1326,7 @@ <h2 id="parameters">Parameters</h2>
affine=self.affine)
nib.save(r1_nifti, base_path + &#39;_r1_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down
6 changes: 3 additions & 3 deletions mapping/t2.html
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Original file line number Diff line number Diff line change
Expand Up @@ -325,7 +325,7 @@ <h1 class="title">Module <code>ukat.mapping.t2</code></h1>
affine=self.affine)
nib.save(r2_nifti, base_path + &#39;_r2_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -844,7 +844,7 @@ <h2 id="parameters">Parameters</h2>
affine=self.affine)
nib.save(r2_nifti, base_path + &#39;_r2_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -955,7 +955,7 @@ <h2 id="parameters">Parameters</h2>
affine=self.affine)
nib.save(r2_nifti, base_path + &#39;_r2_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down
6 changes: 3 additions & 3 deletions mapping/t2star.html
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Original file line number Diff line number Diff line change
Expand Up @@ -346,7 +346,7 @@ <h1 class="title">Module <code>ukat.mapping.t2star</code></h1>
affine=self.affine)
nib.save(r2star_nifti, base_path + &#39;_r2star_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -813,7 +813,7 @@ <h2 id="parameters">Parameters</h2>
affine=self.affine)
nib.save(r2star_nifti, base_path + &#39;_r2star_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down Expand Up @@ -939,7 +939,7 @@ <h2 id="parameters">Parameters</h2>
affine=self.affine)
nib.save(r2star_nifti, base_path + &#39;_r2star_map.nii.gz&#39;)
elif result == &#39;mask&#39;:
mask_nifti = nib.Nifti1Image(self.mask.astype(int),
mask_nifti = nib.Nifti1Image(self.mask.astype(np.uint16),
affine=self.affine)
nib.save(mask_nifti, base_path + &#39;_mask.nii.gz&#39;)
else:
Expand Down
6 changes: 6 additions & 0 deletions mapping/tests/test_b0.html
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Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,8 @@ <h1 class="title">Module <code>ukat.mapping.tests.test_b0</code></h1>
mapper = B0(self.correct_array, self.correct_echo_list,
self.affine, unwrap=False)

if os.path.exists(&#39;test_output&#39;):
shutil.rmtree(&#39;test_output&#39;)
os.makedirs(&#39;test_output&#39;, exist_ok=True)

# Check all is saved.
Expand Down Expand Up @@ -344,6 +346,8 @@ <h2 class="section-title" id="header-classes">Classes</h2>
mapper = B0(self.correct_array, self.correct_echo_list,
self.affine, unwrap=False)

if os.path.exists(&#39;test_output&#39;):
shutil.rmtree(&#39;test_output&#39;)
os.makedirs(&#39;test_output&#39;, exist_ok=True)

# Check all is saved.
Expand Down Expand Up @@ -711,6 +715,8 @@ <h3>Methods</h3>
mapper = B0(self.correct_array, self.correct_echo_list,
self.affine, unwrap=False)

if os.path.exists(&#39;test_output&#39;):
shutil.rmtree(&#39;test_output&#39;)
os.makedirs(&#39;test_output&#39;, exist_ok=True)

# Check all is saved.
Expand Down
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