Merge pull request #201 from UKRIN-MAPS/rel/v0.6.4

rel/v0.6.4

.github/workflows/python_CI.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: [3.8, 3.9]
+        python-version: [3.8, 3.9, "3.10"]
 
     steps:
     - uses: actions/checkout@v2

CHANGELOG.md

@@ -1,3 +1,15 @@
+## [0.6.4] - 2022-11-21
+
+### Added
+* Python 3.10 is now supported.
+
+### Changed
+* Increased upper bounds of M0 in T1, T2 and T2* exponential fit. #196 #199
+* B0 mask now keeps True voxels rather than False voxels, making it align with the rest of UKAT. #194 #195
+
+### Fixed
+* Fixed bug in B0 offset calculation. #200
+
 ## [0.6.3] - 2022-10-26
 
 ### Added

CITATION.cff

@@ -17,7 +17,7 @@ authors:
   given-names: "Susan T"
   orcid: "https://orcid.org/0000-0003-0903-7507"
 title: "UKRIN Kidney Analysis Toolbox"
-version: 0.6.3
+version: 0.6.4
 doi: 10.5281/zenodo.4742470
-date-released: 2022-10-26
+date-released: 2022-11-21
 url: "https://github.com/UKRIN-MAPS/ukat"

README.md

@@ -22,7 +22,7 @@ More information can be found in [this ISMRM abstract](https://www.researchgate.
 # Installing `ukat`
 There are a few different ways you can install `ukat` based on what you want to do with it
 ### "I just want to process my data with this package"
-1. Make sure you're running Python >=3.7
+1. Make sure you're running Python >=3.8
 2. Install `ukat` with `pip install ukat`
 
 ### "I want to modify this code to do something a bit different but don't want my modifications to go back into `ukat`"

setup.py

@@ -10,7 +10,7 @@
 
 setup(
     name="ukat",
-    version="0.6.3",
+    version="0.6.4",
     description="UKRIN Kidney Analysis Toolbox",
     long_description=long_description,
     long_description_content_type="text/markdown",
@@ -31,6 +31,7 @@
         'Operating System :: OS Independent',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
         'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
     ],
 )

ukat/mapping/b0.py

@@ -80,10 +80,10 @@ def __init__(self, pixel_array, echo_list, affine, mask=None,
             # [-pi, pi] if not in that range already.
             self.phase0 = np.ma.masked_array(
                             convert_to_pi_range(np.squeeze(
-                                self.pixel_array[..., 0])), mask=mask)
+                                self.pixel_array[..., 0])), mask=~self.mask)
             self.phase1 = np.ma.masked_array(
                             convert_to_pi_range(np.squeeze(
-                                self.pixel_array[..., 1])), mask=mask)
+                                self.pixel_array[..., 1])), mask=~self.mask)
             if unwrap:
                 # Unwrap each phase image
                 self.phase0 = unwrap_phase(self.phase0,
@@ -97,19 +97,23 @@ def __init__(self, pixel_array, echo_list, affine, mask=None,
             # The following step checks in a central bounding box containing
             # the kidneys if there is an offset in the B0 Map and corrects
             # that offset if it exists. This is due to a jump in phase
-            # that can occurr during the unwrapping of the phase images.
+            # that can occur during the unwrapping of the phase images.
             # Bounding Box
             prop = 0.5
             bx0 = int(self.shape[0] / 2 - prop / 2 * self.shape[0])
             bxf = int(self.shape[0] / 2 + prop / 2 * self.shape[0])
             by0 = int(self.shape[1] / 2 - prop / 2 * self.shape[1])
             byf = int(self.shape[1] / 2 + prop / 2 * self.shape[1])
-            # B0 Map Mean inside the bounding box accross the slices
+            # B0 Map Mean inside the bounding box across the slices
             mean_central_b0 = np.mean(self.b0_map[bx0:bxf, by0:byf, ...])
             # B0 Map Offset Step
             b0_offset_step = 1 / self.delta_te
             # B0 Map Offset Correction
-            self.b0_map -= (mean_central_b0 // b0_offset_step) * b0_offset_step
+            self.b0_map -= (np.round(mean_central_b0 / b0_offset_step)) * \
+                           b0_offset_step
+
+            # Mask B0 Map
+            self.b0_map[np.squeeze(~self.mask)] = 0
         else:
             raise ValueError('The input should contain 2 echo times.'
                              'The last dimension of the input pixel_array must'

ukat/mapping/t1.py

@@ -234,14 +234,14 @@ def __fit_signal__(self, sig, t, parameters):
 
         # Initialise parameters and specify equation to fit to
         if parameters == 2:
-            bounds = ([0, 0], [5000, 10000000])
+            bounds = ([0, 0], [5000, 1000000000])
             initial_guess = [1000, 30000]
             if sig.min() >= 0:
                 eq = two_param_abs_eq
             else:
                 eq = two_param_eq
         elif parameters == 3:
-            bounds = ([0, 0, 1], [5000, 10000000, 2])
+            bounds = ([0, 0, 1], [5000, 1000000000, 2])
             initial_guess = [1000, 30000, 2]
             if sig.min() >= 0:
                 eq = three_param_abs_eq

ukat/mapping/t2.py

@@ -197,11 +197,11 @@ def __fit_signal__(self, sig, te):
         # Initialise parameters
         if self.method == '2p_exp':
             eq = two_param_eq
-            bounds = ([0, 0], [1000, 1000000])
+            bounds = ([0, 0], [1000, 100000000])
             initial_guess = [20, 10000]
         elif self.method == '3p_exp':
             eq = three_param_eq
-            bounds = ([0, 0, 0], [1000, 1000000, 1000000])
+            bounds = ([0, 0, 0], [1000, 100000000, 1000000])
             initial_guess = [20, 10000, 500]
 
         # Fit data to equation

ukat/mapping/t2star.py

@@ -222,7 +222,7 @@ def __fit_signal__(sig, te, method):
 
         elif method == '2p_exp':
             # Initialise parameters
-            bounds = ([0, 0], [700, 1000000])
+            bounds = ([0, 0], [700, 100000000])
             initial_guess = [20, 10000]
 
             # Fit data to equation

ukat/mapping/tests/test_b0.py

@@ -3,6 +3,8 @@
 import numpy as np
 import numpy.testing as npt
 import pytest
+
+from skimage.restoration import unwrap_phase
 from ukat.data import fetch
 from ukat.mapping.b0 import B0
 from ukat.utils import arraystats
@@ -197,8 +199,12 @@ def test_b0_offset_correction(self):
         # Get test data that requires b0_offset correction
         magnitude, phase, affine, te = fetch.b0_siemens(1)
         te *= 1000
+        # Add some extra offset to second TE. B0 maps will be corrupted,
+        # but this still causes the offset correction to be applied.
+        phase[..., 1] = np.angle(
+            np.exp(1j * (unwrap_phase(phase[..., 1]) + np.pi * 1.3)))
         # Process on a central slice only
-        images = phase[:, :, 4, :]
+        images = phase[:, 4, :, :]
         # B0Map with unwrapping
         mapper = B0(images, te, affine, unwrap=True)
         b0_map_without_offset_correction = (mapper.phase_difference /