fmatoolbox 0.2.0__tar.gz → 0.2.1__tar.gz

{fmatoolbox-0.2.0/src/fmatoolbox.egg-info → fmatoolbox-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fmatoolbox
-Version: 0.2.0
+Version: 0.2.1
 Summary: Python port of FMAToolbox
 Author: Pietro Bozzo
 License-Expression: GPL-3.0-or-later

{fmatoolbox-0.2.0 → fmatoolbox-0.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "fmatoolbox"
-version = "0.2.0"
+version = "0.2.1"
 description = "Python port of FMAToolbox"
 authors = [{name = "Pietro Bozzo"}]
 readme = "README.md"

{fmatoolbox-0.2.0 → fmatoolbox-0.2.1}/src/fmatoolbox/data.py

@@ -404,10 +404,12 @@ def saveEvent(session:str|PathLike[str], format:str, data, columns=None, name=No
 
     Args:
         session:    path to session's .xml file, along which the event file will be created
-        format:     format of event file, either:
+        format:     format of event file, parsed as <subdirs>/<name>.<format>, where <subdirs> and <name> are optional, e.g.,
+                    - 'sleep.npy' gives name='sleep', format='npy'
+                    - 'units/firing.wake' gives subdirs='units', name='firing', format='wake'
+                    accepted formats are:
                     - 'npy': DESCRIBE
                     - 'npz': DESCRIBE
-                    - 'name.np#': shorthand for format='np#', name='name'
                     - a different str, to save the event as a text file named <basename>.<format>, prepending a metadata header
                       in this case, `data` must be an array whose columns represent different quantities; if 1d, interpreted as one column
         data:       array to save; for npz format, must be a dict of {'name': array}
@@ -422,23 +424,29 @@ def saveEvent(session:str|PathLike[str], format:str, data, columns=None, name=No
         saveEvent(session, 'npz', {'onset':[1,2], 'offset':[1.5,3]}, name='sleep')
         # or
         saveEvent(session, 'sleep.npz', {'onset':[1,2], 'offset':[1.5,3]})
+
+        # save the same file in subdirectory 'new' within the session
+        saveEvent(session, 'new/sleep.npz', {'onset':[1,2], 'offset':[1.5,3]})
     """
 
     # parse format
-    parts = format.rsplit('.', 1)
-    format = parts[-1]
-    if len(parts) > 1: name = parts[0]
+    subdirs, _, filename = format.rpartition('/')
+    name, dot, format = filename.rpartition('.')
+    if not dot:
+        name, format = '', filename
+    session = pathlib.Path(session)
+    froot = session.parent / subdirs / session.stem
 
     if format == 'npy' or format == 'npz':
-        if name is None:
+        if not name:
             raise ValueError(f"'name' must be specified for {format} format")
-        fname = pathlib.Path(session).with_suffix(f'.{name}.{format}')
+        fname = froot.with_suffix(f'.{name}.{format}')
         np.save(fname, data) if format == 'npy' else np.savez(fname, **data)
 
     else:
         if columns is None:
             raise ValueError("'columns' must be specified for text formats")
-        fname = pathlib.Path(session).with_suffix(f'.{format}')
+        fname = froot.with_suffix(f'.{format}')
         np.savetxt(fname, data, delimiter=',', header=f" columns: {', '.join(columns)}", comments="%")
 
     return

{fmatoolbox-0.2.0 → fmatoolbox-0.2.1}/src/fmatoolbox/general.py

@@ -1,6 +1,7 @@
 """ General-purpose data processing for FMAToolbox """
 
 import numpy as np
+import fmatoolbox.intervals
 
 
 def unwhere(indices,shape=None):
@@ -50,7 +51,7 @@ def shuffleEvents(events, offset:float=None, n:int=None, group=None, fast:bool=N
     if n is None: n = 1
     if group is not None: group = np.asarray(group,dtype=int)
     if intervals is not None:
-        events, valid = restrict(events,intervals,shift=True,s_ind=True)
+        events, valid = fmatoolbox.intervals.restrict(events,intervals,shift=True,s_ind=True)
         offset = 0
         if group is not None:
             group = group[valid]
@@ -107,7 +108,7 @@ def shuffleEvents(events, offset:float=None, n:int=None, group=None, fast:bool=N
     # unshift events back into intervals
     if intervals is not None:
         for i in range(n):
-            shuffled[:,:,i] = unshift(shuffled[:,:,i],intervals)
+            shuffled[:,:,i] = fmatoolbox.intervals.unshift(shuffled[:,:,i],intervals)
 
     # restore shape
     if n_dim == 1 and n == 1:

{fmatoolbox-0.2.0 → fmatoolbox-0.2.1}/src/fmatoolbox/plotting.py

@@ -33,10 +33,10 @@ def adjustAxes(axs:Axes|Iterable[Axes], format:Literal['paper','poster']='paper'
     lw = 0.6 if format == 'paper' else 2
     ax_title_fs = 7 if format == 'paper' else 18
     ax_label_fs = 7 if format == 'paper' else 18
-    ax_label_pad = 0.1 if format == 'paper' else 1
-    ax_tick_fs = 6 if format == 'paper' else 14
+    ax_label_pad = 1 if format == 'paper' else 1
+    ax_tick_fs = 5 if format == 'paper' else 14
     ax_tick_l = 2 if format == 'paper' else 5
-    ax_tick_pad = 1 if format == 'paper' else 2
+    ax_tick_pad = 2 if format == 'paper' else 2
 
     for ax in axs:
         
@@ -266,7 +266,8 @@ def plotColorMap(data:ArrayLike, vmin:float=None, vmax:float=None, zscore=None,
         smooth          float | (float,float) = None, standard deviation of gaussian kernel passed to ``scipy.ndimage.gaussian_filter`` (after zoom)
         alpha           float | (n,m) float = None, transparency mask for `data` (e.g., to show significance of pixels), values must be in [0,1]
         x, y            (:,) float, coordinates corresponding to columns and rows of `data`, defaults are range(m) and range(n)
-        aspect          str | float | None, same behavior as aspect parameter of imshow
+        aspect          str | float | None, same behavior as aspect parameter of imshow, 'auto' to keep axis aspect ration,
+                        'preserve' to keep it even when a colorbar is drawn
         bar             str = None, if given, draw colorbar next to `ax` with label specified by `bar`, and return both `im` and `cb` objects
         barticks        (:,) float, if given, draw colorbar next to `ax` with ticks specified by `barticks`, and return both `im` and `cb` objects
         ax              matplotlib.axes.Axes = matplotlib.pyplot.gca(), axes to plot in
@@ -276,7 +277,10 @@ def plotColorMap(data:ArrayLike, vmin:float=None, vmax:float=None, zscore=None,
         cb              colorbar, optional
     """
 
-    data = np.array(data,ndmin=2)
+    data = np.array(data, ndmin=2)
+    if ax is None:
+        ax = plt.gca()
+    bb = ax.get_position()
 
     # 1. z-score
     if zscore is not None:
@@ -323,9 +327,9 @@ def plotColorMap(data:ArrayLike, vmin:float=None, vmax:float=None, zscore=None,
         dy = 0.5
     else:
         dy = 0.5 if n_y == 1 else (y[-1] - y[0]) / (data.shape[0] - 1) / 2
-    if ax is None:
-        ax = plt.gca()
 
+    restore = aspect == 'preserve'
+    if restore: aspect = 'auto'
     im = ax.imshow(data, aspect=aspect, vmin=vmin, vmax=vmax, origin='lower', extent=[x[0]-dx, x[-1]+dx, y[0]-dy, y[-1]+dy], **kwargs)
     if alpha is not None:
         im.set_alpha(alpha)
@@ -333,6 +337,8 @@ def plotColorMap(data:ArrayLike, vmin:float=None, vmax:float=None, zscore=None,
         cb = plt.colorbar(im, label=bar, ticks=barticks, ax=ax)
         cb.set_label(bar)
         adjustAxes(cb.ax)
+    if restore:
+        ax.set_position(bb) # restore position (modified by plt.colorbar)
 
     # plot peaks
     if isinstance(sortby,str) and sortby == 'peak-show':
@@ -555,7 +561,7 @@ def boxPlot(data:ArrayLike|Sequence[ArrayLike], x:ArrayLike=None, mode:Literal['
         for col in color:
             r, g, b, a = mplc.to_rgba(col)
             facecolor.append((r,g,b,a*0.5))
-        kwargs.setdefault('widths', 0.8)
+        kwargs.setdefault('widths', 1)
         vp = ax.violinplot(data_clean, positions=x, side='high', facecolor=facecolor, linecolor=color,
                            showmedians=True, showextrema=False, **kwargs)
         out.append(vp)
@@ -656,7 +662,7 @@ def pBar(p:ArrayLike, x:ArrayLike=None, alpha:float=None, dy:float=None, draw:Se
 def pHorzLine(p, t=None, dy=None, color:ColorType=None, ax:Axes=None, **kwargs):
     """draw a horizontal line indicating time points where time series passed a statistical test
 
-    arguments:
+    Args:
         p           (t,c) bool, decision of a statistical test, t: number of time points, c: number of conditions
         t           (t,) float = range(n), time points
         dy          float, scale vertical distances between bars
@@ -695,7 +701,7 @@ def pHorzLine(p, t=None, dy=None, color:ColorType=None, ax:Axes=None, **kwargs):
 
 def plotIntervals(intervals, color:ColorType='gray', alpha=0.3, label:str=None, ax:Axes=None, **plot_kwargs):
 
-    intervals = fmatoolbox.intervals.consolidateIntervals(intervals)
+    intervals = fmatoolbox.intervals.consolidate(intervals)
     if intervals.size == 0:
         return
     if ax is None:

{fmatoolbox-0.2.0 → fmatoolbox-0.2.1}/src/fmatoolbox/regions.py

@@ -574,7 +574,7 @@ class regions:
     
 
     def avalanches(self, regs=None, when=None, thresh:float=None, bin_mode:Literal['fixed','isi']=None, window:float=None, step:int=None,
-                   shift:bool=None, smooth:bool=None, norm:bool=None, return_fr:bool=None):
+                   shift:bool=None, smooth:float=None, norm:bool=None, return_fr:bool=None):
         """compute avalanches per region from population firing rate
 
         arguments:

{fmatoolbox-0.2.0 → fmatoolbox-0.2.1/src/fmatoolbox.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fmatoolbox
-Version: 0.2.0
+Version: 0.2.1
 Summary: Python port of FMAToolbox
 Author: Pietro Bozzo
 License-Expression: GPL-3.0-or-later