bump version, merge pull request #27 from AMYPAD/devel

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.1.0
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -31,16 +31,19 @@ repos:
   - id: flake8
     args: [-j8]
     additional_dependencies:
+    - flake8-broken-line
     - flake8-bugbear
     - flake8-comprehensions
     - flake8-debugger
+    - flake8-isort
     - flake8-string-format
 - repo: https://github.com/google/yapf
-  rev: v0.31.0
+  rev: v0.32.0
   hooks:
   - id: yapf
     args: [-i]
+    additional_dependencies: [toml]
 - repo: https://github.com/PyCQA/isort
-  rev: 5.9.3
+  rev: 5.10.1
   hooks:
   - id: isort

miutil/fdio.py

@@ -78,6 +78,7 @@ def extractall(fzip, dest, desc="Extracting"):
 
 def nsort(fnames):
     """Sort a file list, automatically detecting embedded numbers"""
+
     def path2parts(fname):
         parts = re.split(r"([0-9][0-9.]*e[-+][0-9]+|[0-9]+\.[0-9]+|[0-9]+)", fname)
         parts[1::2] = map(float, parts[1::2])

miutil/imio/nii.py

@@ -55,7 +55,7 @@ def nii_gzip(imfile, outpath=""):
     return fout
 
 
-def getnii(fim, nan_replace=None, output="image"):
+def getnii(fim, nan_replace=None, output='image'):
     """
     Get PET image from NIfTI file.
     Arguments:
@@ -71,10 +71,10 @@ def getnii(fim, nan_replace=None, output="image"):
     """
     nim = nib.load(fspath(fim))
 
-    dim = nim.header.get("dim")
+    dim = nim.header.get('dim')
     dimno = dim[0]
 
-    if output == "image" or output == "all":
+    if output == 'image' or output == 'all':
         imr = np.asanyarray(nim.dataobj)
         # replace NaNs if requested
         if isinstance(nan_replace, numbers.Number):
@@ -86,38 +86,37 @@ def getnii(fim, nan_replace=None, output="image"):
 
         # > get orientations from the affine
         ornt = nib.io_orientation(nim.affine)
-        trnsp = tuple(2 - np.int8(ornt[:, 0]))
+        trnsp = tuple(np.int8([ornt[2, 0], ornt[1, 0], ornt[0, 0]]))
         flip = tuple(np.int8(ornt[:, 1]))
 
         # > voxel size
-        voxsize = nim.header.get("pixdim")[1:nim.header.get("dim")[0] + 1]
+        voxsize = nim.header.get('pixdim')[1:nim.header.get('dim')[0] + 1]
         # > rearrange voxel size according to the orientation
         voxsize = voxsize[np.array(trnsp)]
 
         # > dimensions
-        dims = dim[1:nim.header.get("dim")[0] + 1]
+        dims = dim[1:nim.header.get('dim')[0] + 1]
         dims = dims[np.array(trnsp)]
 
-        # > flip y-axis and z-axis and then transpose.
-        # Depends if dynamic (4 dimensions) or static (3 dimensions)
-        if dimno == 4:
+        # > flip y-axis and z-axis and then transpose
+        if dimno == 4:   # dynamic
             imr = np.transpose(imr[::-flip[0], ::-flip[1], ::-flip[2], :], (3,) + trnsp)
-        elif dimno == 3:
+        elif dimno == 3: # static
             imr = np.transpose(imr[::-flip[0], ::-flip[1], ::-flip[2]], trnsp)
 
-    if output == "affine" or output == "all":
+    if output == 'affine' or output == 'all':
         # A = nim.get_sform()
         # if not A[:3,:3].any():
         #     A = nim.get_qform()
         A = nim.affine
 
-    if output == "all":
+    if output == 'all':
         out = {
-            "im": imr, "affine": A, "fim": fim, "dtype": nim.get_data_dtype(), "shape": imr.shape,
-            "hdr": nim.header, "voxsize": voxsize, "dims": dims, "transpose": trnsp, "flip": flip}
-    elif output == "image":
+            'im': imr, 'affine': A, 'fim': fim, 'dtype': nim.get_data_dtype(), 'shape': imr.shape,
+            'hdr': nim.header, 'voxsize': voxsize, 'dims': dims, 'transpose': trnsp, 'flip': flip}
+    elif output == 'image':
         out = imr
-    elif output == "affine":
+    elif output == 'affine':
         out = A
     else:
         raise NameError("Unrecognised output request!")
@@ -154,15 +153,12 @@ def array2nii(im, A, fnii, descrip="", trnsp=None, flip=None, storage_as=None):
     # >>as obtained from getnii(..., output='all')
 
     # > permute the axis order in the image array
-    if (isinstance(storage_as, dict) and "transpose" in storage_as and "flip" in storage_as):
+    if (isinstance(storage_as, dict) and 'transpose' in storage_as and 'flip' in storage_as):
 
-        trnsp = (
-            storage_as["transpose"].index(0),
-            storage_as["transpose"].index(1),
-            storage_as["transpose"].index(2),
-        )
+        trnsp = (storage_as['transpose'].index(0), storage_as['transpose'].index(1),
+                 storage_as['transpose'].index(2))
 
-        flip = storage_as["flip"]
+        flip = storage_as['flip']
 
     if not trnsp:
         im = im.transpose()
@@ -179,10 +175,10 @@ def array2nii(im, A, fnii, descrip="", trnsp=None, flip=None, storage_as=None):
 
     res = nib.Nifti1Image(im, A)
     hdr = res.header
-    hdr.set_sform(None, code="scanner")
-    hdr["cal_max"] = np.max(im) # np.percentile(im, 90) #
-    hdr["cal_min"] = np.min(im)
-    hdr["descrip"] = descrip
+    hdr.set_sform(None, code='scanner')
+    hdr['cal_max'] = np.max(im) # np.percentile(im, 90) #
+    hdr['cal_min'] = np.min(im)
+    hdr['descrip'] = descrip
     nib.save(res, fspath(fnii))
 
 
@@ -255,23 +251,23 @@ def niisort(fims, memlim=True):
         raise ValueError("Input image(s) must be 3D.")
 
     out = {
-        "shape": _nii.shape[::-1], "files": _fims, "sortlist": sortlist,
-        "dtype": _nii.get_data_dtype(), "N": Nim}
+        'shape': _nii.shape[::-1], 'files': _fims, 'sortlist': sortlist,
+        'dtype': _nii.get_data_dtype(), 'N': Nim}
 
     if memlim and Nfrm > 50:
-        imdic = getnii(_fims[0], output="all")
-        affine = imdic["affine"]
+        imdic = getnii(_fims[0], output='all')
+        affine = imdic['affine']
     else:
         # get the images into an array
         _imin = np.zeros((Nfrm,) + _nii.shape[::-1], dtype=_nii.get_data_dtype())
         for i in range(Nfrm):
             if i in sortlist:
-                imdic = getnii(_fims[i], output="all")
-                _imin[i, :, :, :] = imdic["im"]
-                affine = imdic["affine"]
-        out["im"] = _imin[:Nfrm, :, :, :]
+                imdic = getnii(_fims[i], output='all')
+                _imin[i, :, :, :] = imdic['im']
+                affine = imdic['affine']
+        out['im'] = _imin[:Nfrm, :, :, :]
 
-    out["affine"] = affine
+    out['affine'] = affine
 
     return out
 

miutil/plot.py

@@ -43,9 +43,10 @@ class imscroll:
     """
 
     _instances = []
-    _SUPPORTED_KEYS = ["control", "shift"]
+    _SUPPORTED_KEYS = ['control', 'shift']
 
-    def __init__(self, vol, view="t", fig=None, titles=None, order=0, **kwargs):
+    def __init__(self, vol, view='t', fig=None, titles=None, order=0, sharexy=None, show=False,
+                 **kwargs):
         """
         Scroll through 2D slices of 3D volume(s) using the mouse.
         Args:
@@ -56,6 +57,8 @@ def __init__(self, vol, view="t", fig=None, titles=None, order=0, **kwargs):
             titles (list): list of strings (overrides `vol.keys()`).
             order (int): spline interpolation order for line profiles.
                 0: nearest, 1: bilinear, >2: probably avoid.
+            sharexy (bool): whether to link zoom across all axes.
+            show (bool): whether to run `matplotlib.pyplot.show()`.
             **kwargs: passed to `matplotlib.pyplot.imshow()`.
         """
         if isinstance(vol, str) and path.exists(vol):
@@ -79,19 +82,21 @@ def __init__(self, vol, view="t", fig=None, titles=None, order=0, **kwargs):
                 """.format(ndim)))
 
         view = view.lower()
-        if view in ["c", "coronal", "y"]:
+        if view in ['c', 'coronal', 'y']:
             vol = [i.transpose(1, 0, 2) for i in vol]
-        elif view in ["s", "saggital", "x"]:
+        elif view in ['s', 'saggital', 'x']:
             vol = [i.transpose(2, 0, 1) for i in vol]
 
         # volumes
         self.titles = titles or [None] * len(vol)
         self.index_max = min(map(len, vol))
         self.index = self.index_max // 2
+        if sharexy is None:
+            sharexy = len({i.shape for i in vol}) == 1
         if fig is not None:
-            self.fig, axs = fig, fig.subplots(1, len(vol))
+            self.fig, axs = fig, fig.subplots(1, len(vol), sharex=sharexy, sharey=sharexy)
         else:
-            self.fig, axs = plt.subplots(1, len(vol))
+            self.fig, axs = plt.subplots(1, len(vol), sharex=sharexy, sharey=sharexy)
         self.axs = [axs] if len(vol) == 1 else list(axs.flat)
         for ax, i, t in zip(self.axs, vol, self.titles):
             ax.imshow(i[self.index], **kwargs)
@@ -103,28 +108,30 @@ def __init__(self, vol, view="t", fig=None, titles=None, order=0, **kwargs):
         self._annotes = []
         # event callbacks
         self.key = {i: False for i in self._SUPPORTED_KEYS}
-        self.fig.canvas.mpl_connect("scroll_event", self._scroll)
-        self.fig.canvas.mpl_connect("key_press_event", self._on_key)
-        self.fig.canvas.mpl_connect("key_release_event", self._off_key)
-        self.fig.canvas.mpl_connect("button_press_event", self._on_click)
+        self.fig.canvas.mpl_connect('scroll_event', self._scroll)
+        self.fig.canvas.mpl_connect('key_press_event', self._on_key)
+        self.fig.canvas.mpl_connect('key_release_event', self._off_key)
+        self.fig.canvas.mpl_connect('button_press_event', self._on_click)
         imscroll._instances.append(self) # prevents gc
+        if show:
+            plt.show()
 
     @classmethod
     def clear(cls, self):
         cls._instances.clear()
 
     def _on_key(self, event):
-        key = {"ctrl": "control"}.get(event.key, event.key)
+        key = {'ctrl': 'control'}.get(event.key, event.key)
         if key in self._SUPPORTED_KEYS:
             self.key[key] = True
 
     def _off_key(self, event):
-        key = {"ctrl": "control"}.get(event.key, event.key)
+        key = {'ctrl': 'control'}.get(event.key, event.key)
         if key in self._SUPPORTED_KEYS:
             self.key[key] = False
 
     def _scroll(self, event):
-        self.set_index(self.index + event.step * (10 if self.key["shift"] else 1))
+        self.set_index(self.index + event.step * (10 if self.key['shift'] else 1))
 
     def set_index(self, index):
         self.index = int(index) % self.index_max
@@ -137,7 +144,7 @@ def set_index(self, index):
         self.fig.canvas.draw()
 
     def _on_click(self, event):
-        if not self.key["control"] or None in (event.xdata, event.ydata):
+        if not self.key['control'] or None in (event.xdata, event.ydata):
             return
         self.picked.append((event.xdata, event.ydata))
         if len(self.picked) < 2:
@@ -156,20 +163,20 @@ def _on_click(self, event):
                     arr,
                     np.vstack((x, y, np.ones_like(x) * i)),
                     order=self.order,
-                    mode="nearest",
+                    mode='nearest',
                 ) for i in range(event.inaxes.images[0].get_array().shape[-1])]
         else:
-            z = ndi.map_coordinates(arr, np.vstack((x, y)), order=self.order, mode="nearest")
+            z = ndi.map_coordinates(arr, np.vstack((x, y)), order=self.order, mode='nearest')
         self.picked = []
-        self.key["control"] = False
+        self.key['control'] = False
 
-        self._annotes.append(event.inaxes.plot([x0, x1], [y0, y1], "r-")[0])
+        self._annotes.append(event.inaxes.plot([x0, x1], [y0, y1], 'r-')[0])
         plt.figure()
         if arr.ndim == 3:
-            for channel, colour in zip(z, "rgbcmyk"):
-                plt.plot(x, channel, colour + "-")
+            for channel, colour in zip(z, 'rgbcmyk'):
+                plt.plot(x, channel, colour + '-')
         else:
-            plt.plot(x, z, "r-")
+            plt.plot(x, z, 'r-')
         plt.xlabel("x")
         plt.ylabel("Intensity")
         plt.show()

pyproject.toml

@@ -1,6 +1,5 @@
 [build-system]
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
-build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 write_to = "miutil/_dist_ver.py"