pyMapVBVD 0.5.6__tar.gz → 0.6.0__tar.gz

{pyMapVBVD-0.5.6 → pymapvbvd-0.6.0}/CHANGELOG.md

@@ -1,5 +1,16 @@
 This document contains the pymapvbvd release history in reverse chronological order.
 
+0.6.0 (Friday 28th June 2024)
+-----------------------------
+- Dropped support for Python 3.8
+- Testing for Python 3.12
+- Compatibility with Numpy version 2
+
+0.5.7 (Wednesday 31st January 2024)
+-----------------------------------
+- Added flag to disable line reflection. Thanks to FrankZijlstra for contributing.
+- Fixed depreciation warning (Issue 42). Thanks to MusicInMyBrain for reporting. 
+
 0.5.6 (Wednesday 11th October 2023)
 -----------------------------------
 - Fixed issue with large files on Windows. Thanks to FrankZijlstra for reporting.

{pyMapVBVD-0.5.6/pyMapVBVD.egg-info → pymapvbvd-0.6.0}/PKG-INFO

@@ -1,23 +1,23 @@
 Metadata-Version: 2.1
 Name: pyMapVBVD
-Version: 0.5.6
+Version: 0.6.0
 Summary: Python twix file reader
 Home-page: https://github.com/wtclarke/pymapvbvd
 Author: Will Clarke
 Author-email: william.clarke@ndcn.ox.ac.uk
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
+Requires-Dist: numpy>=1.26
 Requires-Dist: tqdm
-Requires-Dist: scipy
+Requires-Dist: scipy==1.13.*
 Requires-Dist: matplotlib
 Requires-Dist: h5py
 Requires-Dist: six

{pyMapVBVD-0.5.6 → pymapvbvd-0.6.0}/mapvbvd/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-10-11T11:46:40+0100",
+ "date": "2024-06-28T18:18:24+0100",
  "dirty": false,
  "error": null,
- "full-revisionid": "d5a034974529cbe263fcacfd6e269b6830d3f7e6",
- "version": "0.5.6"
+ "full-revisionid": "d4a4ec98f970a140ffe9984fafe6fd5f793fbfca",
+ "version": "0.6.0"
 }
 '''  # END VERSION_JSON
 

{pyMapVBVD-0.5.6 → pymapvbvd-0.6.0}/mapvbvd/mapVBVD.py

@@ -108,7 +108,7 @@ def loop_mdh_read(fid, version, Nscans, scan, measOffset, measLength, print_prog
             data_u8[3] = get_bit(data_u8[3], 0)  # ubit24: keep only 1 bit from the 4th byte
             tmp = data_u8[0:4]
             tmp.dtype = np.uint32
-            ulDMALength = float(tmp)
+            ulDMALength = tmp.item()
 
             if (ulDMALength == 0) or (bitMask & bit_0):
                 cPos = cPos + ulDMALength
@@ -122,7 +122,7 @@ def loop_mdh_read(fid, version, Nscans, scan, measOffset, measLength, print_prog
             data_u8[3] = get_bit(data_u8[3], 0)  # ubit24: keep only 1 bit from the 4th byte
             tmp = data_u8[0:4]
             tmp.dtype = np.uint32
-            ulDMALength = float(tmp)
+            ulDMALength = tmp.item()
             cPos = cPos + ulDMALength
             continue
 
@@ -132,9 +132,7 @@ def loop_mdh_read(fid, version, Nscans, scan, measOffset, measLength, print_prog
         #          the "DMA length"
         #              if mdh.ulPackBit
         #          it seems that the packbit is not always set correctly
-        tmp = data_u8[dmaIdx]
-        tmp.dtype = np.uint16
-        NCol_NCha = tmp  # was float [ushSamplesInScan  ushUsedChannels]
+        NCol_NCha = data_u8[dmaIdx].view(np.uint16).astype(int)
         ulDMALength = dmaOff + (8 * NCol_NCha[0] + dmaSkip) * NCol_NCha[1]
 
         n_acq = n_acq + 1
@@ -340,8 +338,8 @@ def mapVBVD(filename, quiet=False, **kwargs):
         measOffset = np.zeros(NScans, dtype=np.uint64)
         measLength = np.zeros(NScans, dtype=np.uint64)
         for k in range(NScans):
-            measOffset[k] = np.fromfile(fid, dtype=np.uint64, count=1, offset=0)
-            measLength[k] = np.fromfile(fid, dtype=np.uint64, count=1, offset=0)
+            measOffset[k] = np.fromfile(fid, dtype=np.uint64, count=1, offset=0).item()
+            measLength[k] = np.fromfile(fid, dtype=np.uint64, count=1, offset=0).item()
             fid.seek(152 - 16, 1)
 
     else:

{pyMapVBVD-0.5.6 → pymapvbvd-0.6.0}/mapvbvd/read_twix_hdr.py

@@ -1,6 +1,6 @@
 import re
 import numpy as np
-from scipy.integrate import cumtrapz
+from scipy.integrate import cumulative_trapezoid
 
 from mapvbvd._attrdict import AttrDict
 
@@ -231,7 +231,7 @@ def read_twix_hdr(fid, prot):
 
             # make sure that gr_adc is always positive (rstraj needs to be strictly monotonic)
             gr_adc = np.maximum(gr_adc, 1e-4)
-            rstraj = (np.append(0, cumtrapz(gr_adc)) - ncol / 2) / np.sum(gr_adc)
+            rstraj = (np.append(0, cumulative_trapezoid(gr_adc)) - ncol / 2) / np.sum(gr_adc)
             rstraj -= np.mean(rstraj[int(ncol / 2) - 1:int(ncol / 2) + 1])
             # scale rstraj by kmax (only works if all slices have same FoV!!!)
             # TODO: these are examples of the keys not arranged correctly

{pyMapVBVD-0.5.6 → pymapvbvd-0.6.0}/mapvbvd/twix_map_obj.py

@@ -153,6 +153,14 @@ class twix_map_obj:
             raise Exception('No trajectory for regridding available')
         self.regrid = bval
 
+    @property
+    def flagDisableReflect(self):
+        return self.disableReflect
+
+    @flagDisableReflect.setter
+    def flagDisableReflect(self, val):
+        self.disableReflect = val
+
     # TODO: flagDoRawDataCorrect
     @property
     def flagDoRawDataCorrect(self):
@@ -181,6 +189,7 @@ class twix_map_obj:
         self.averageSets = kwargs.get('averageSets', False)
         self.ignoreSeg = kwargs.get('ignoreSeg', False)
         self.squeeze = kwargs.get('squeeze', False)
+        self.disableReflect = kwargs.get('disableReflect', False)
 
         self.dType = dataType.lower()
         self.fname = fname
@@ -806,8 +815,9 @@ class twix_map_obj:
                 # if  bDoRawDataCorrect && bIsRawDataCorrect(k): WTC: not implemented yet
 
                 # reflect fids when necessary
-                isRefl = np.where(bIsReflected[ix])[0]
-                block[:, :, isRefl] = block[-1::-1, :, isRefl]
+                if not self.disableReflect:
+                    isRefl = np.where(bIsReflected[ix])[0]
+                    block[:, :, isRefl] = block[-1::-1, :, isRefl]
 
                 if bRegrid:
                     # correct for readout shifts

{pyMapVBVD-0.5.6 → pymapvbvd-0.6.0/pyMapVBVD.egg-info}/PKG-INFO

@@ -1,23 +1,23 @@
 Metadata-Version: 2.1
 Name: pyMapVBVD
-Version: 0.5.6
+Version: 0.6.0
 Summary: Python twix file reader
 Home-page: https://github.com/wtclarke/pymapvbvd
 Author: Will Clarke
 Author-email: william.clarke@ndcn.ox.ac.uk
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
+Requires-Dist: numpy>=1.26
 Requires-Dist: tqdm
-Requires-Dist: scipy
+Requires-Dist: scipy==1.13.*
 Requires-Dist: matplotlib
 Requires-Dist: h5py
 Requires-Dist: six

{pyMapVBVD-0.5.6 → pymapvbvd-0.6.0}/pyMapVBVD.egg-info/requires.txt

@@ -1,6 +1,6 @@
-numpy
+numpy>=1.26
 tqdm
-scipy
+scipy==1.13.*
 matplotlib
 h5py
 six

{pyMapVBVD-0.5.6 → pymapvbvd-0.6.0}/requirements.yml

@@ -1,7 +1,7 @@
 dependencies:
- - numpy
+ - numpy>=1.26
  - tqdm
- - scipy
+ - scipy==1.13.*
  - matplotlib
  - h5py
  - six

{pyMapVBVD-0.5.6 → pymapvbvd-0.6.0}/setup.py

@@ -31,10 +31,10 @@ setuptools.setup(
     license_file='LICENSE',
     classifiers=[
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent", ],
-    python_requires='>=3.8')
+    python_requires='>=3.9')