bump verison, merge branch 'devel'

README.rst

@@ -16,6 +16,7 @@ Intended for inclusion in requirements for other packages.
 The package name is ``miutil``. Options include:
 
 - nii
+- plot
 
 To install options and their dependencies,
 use the package name ``miutil[option1,option2]``.

miutil/imio/__init__.py

@@ -0,0 +1,20 @@
+import re
+
+RE_NII_GZ = re.compile(r"^(.+)(\.nii(?:\.gz)?)$", flags=re.I)
+RE_NPYZ = re.compile(r"^(.+)(\.np[yz])$", flags=re.I)
+
+
+def imread(fname):
+    """Read any supported filename"""
+    if RE_NII_GZ.search(fname):
+        from .nii import getnii
+
+        return getnii(fname)
+    elif RE_NPYZ.search(fname):
+        import numpy as np
+
+        res = np.load(fname)
+        if hasattr(res, "keys") and len(res.keys()) == 1:
+            res = res[list(res.keys())[0]]
+        return res
+    raise ValueError("Unknown image type: " + fname)

miutil/imio/nii.py

@@ -9,9 +9,9 @@
 import nibabel as nib
 import numpy as np
 
+from . import RE_NII_GZ
 from ..fdio import create_dir
 
-RE_NII_GZ = re.compile(r"^(.+)(\.nii(?:\.gz)?)$", flags=re.I)
 RE_GZ = re.compile(r"^(.+)(\.gz)$", flags=re.I)
 log = logging.getLogger(__name__)
 

miutil/plot.py

@@ -0,0 +1,87 @@
+from os import path
+import matplotlib.pyplot as plt
+
+from .imio import imread
+
+
+class imscroll:
+    """
+    Slice through volumes by scrolling.
+    Hold SHIFT to scroll faster.
+    """
+
+    instances = []
+    SUPPORTED_KEYS = ["shift"]
+
+    def __init__(self, vol, view="t", fig=None, titles=None, **kwargs):
+        """
+        Scroll through 2D slices of 3D volume(s) using the mouse.
+        Args:
+            vol (str or numpy.ndarray or list or dict): path to file or
+                a (list/dict of) array(s).
+            view (str): z, t, transverse/y, c, coronal/x, s, sagittal.
+            fig (matplotlib.pyplot.Figure): will be created if unspecified.
+            titles (list): list of strings (overrides `vol.keys()`).
+            **kwargs: passed to `matplotlib.pyplot.imshow()`.
+        """
+        if isinstance(vol, str) and path.exists(vol):
+            vol = imread(vol)
+        if hasattr(vol, "keys"):
+            keys = list(vol.keys())
+            vol = [vol[i] for i in keys]
+            if titles is None:
+                titles = keys
+        if vol[0].ndim == 2:
+            vol = [vol]
+        elif vol[0].ndim != 3:
+            raise IndexError("Expected vol.ndim in [3, 4] but got {}".format(vol.ndim))
+
+        self.titles = titles or [None] * len(vol)
+
+        view = view.lower()
+        if view in ["c", "coronal", "y"]:
+            vol = [i.transpose(1, 0, 2) for i in vol]
+        elif view in ["s", "saggital", "x"]:
+            vol = [i.transpose(2, 0, 1) for i in vol]
+
+        self.index_max = min(map(len, vol))
+        self.index = self.index_max // 2
+        if fig is not None:
+            self.fig, axs = fig, fig.subplots(1, len(vol))
+        else:
+            self.fig, axs = plt.subplots(1, len(vol))
+        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)
+            ax.set_title(t or "slice #{}".format(self.index))
+        self.vols = vol
+        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)
+        imscroll.instances.append(self)  # prevents gc
+
+    @classmethod
+    def clear(cls, self):
+        cls.instances.clear()
+
+    def on_key(self, event):
+        if event.key in self.SUPPORTED_KEYS:
+            self.key[event.key] = True
+
+    def off_key(self, event):
+        if event.key in self.SUPPORTED_KEYS:
+            self.key[event.key] = False
+
+    def scroll(self, event):
+        self.set_index(
+            self.index
+            + (1 if event.button == "up" else -1) * (10 if self.key["shift"] else 1)
+        )
+
+    def set_index(self, index):
+        self.index = index % self.index_max
+        for ax, vol, t in zip(self.axs, self.vols, self.titles):
+            ax.images[0].set_array(vol[self.index])
+            ax.set_title(t or "slice #{}".format(self.index))
+        self.fig.canvas.draw()

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = miutil
-version = 0.1.0
+version = 0.2.0
 description = Medical imaging utilities for the AMYPAD and NiftyPET projects
 long_description = file: README.rst
 license = Apache 2.0
@@ -48,6 +48,8 @@ dev =
 nii =
     nibabel
     numpy
+plot =
+    matplotlib
 
 [flake8]
 max_line_length = 88

tests/test_imio.py

@@ -0,0 +1,19 @@
+from pytest import importorskip
+
+from miutil.imio import imread
+
+
+def test_imread(tmp_path):
+    np = importorskip("numpy")
+
+    x = np.random.randint(10, size=(9, 9))
+    fname = tmp_path / "test_imread.npy"
+    np.save(fname, x)
+    assert (imread(str(fname)) == x).all()
+
+    fname = tmp_path / "test_imread.npz"
+    np.savez(fname, x)
+    assert (imread(str(fname)) == x).all()
+
+    np.savez(fname, x, x)
+    assert (imread(str(fname))["arr_0"] == x).all()