updates to gallery

Author: zm711

.gitignore

@@ -76,4 +76,8 @@ doc/*.plx
 doc/*.nev
 doc/*.ns5
 doc/*.nix
-doc/*.nwb
+doc/*.nwb
+*.plx
+*.smr
+B95.zip
+grouped_ephys

doc/source/conf.py

@@ -252,6 +252,7 @@
 )
 
 sphinx_gallery_conf = {
+    'only_warn_on_example_error': True, # helps with debugging broken examples
     "examples_dirs": "../../examples",  # path to your example scripts
     "gallery_dirs": "examples",  # path to where to save gallery generated output
 }

examples/igorio.py

@@ -29,3 +29,5 @@
 plt.plot(signal.times, signal)
 plt.xlabel(signal.sampling_period.dimensionality)
 plt.ylabel(signal.dimensionality)
+
+plt.show()

examples/imageseq.py

@@ -24,9 +24,9 @@
 image_seq = ImageSequence(l, sampling_rate=500 * pq.Hz, spatial_scale="m", units="V")
 
 result = image_seq.signal_from_region(
-    CircularRegionOfInterest(50, 50, 25),
-    CircularRegionOfInterest(10, 10, 5),
-    PolygonRegionOfInterest((50, 25), (50, 45), (14, 65), (90, 80)),
+    CircularRegionOfInterest(image_seq,50, 50, 25),
+    CircularRegionOfInterest(image_seq, 10, 10, 5),
+    PolygonRegionOfInterest(image_seq,(50, 25), (50, 45), (14, 65), (90, 80)),
 )
 
 for i in range(len(result)):

examples/roi_demo.py

@@ -6,10 +6,24 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-from neo.core import CircularRegionOfInterest, RectangularRegionOfInterest, PolygonRegionOfInterest
+from neo.core import CircularRegionOfInterest, RectangularRegionOfInterest, PolygonRegionOfInterest, ImageSequence
 from numpy.random import rand
+import random
+import quantities as pq
 
 
+# First we create our image_sequence. Let's generate some data
+
+l = []
+for frame in range(50):
+    l.append([])
+    for y in range(100):
+        l[frame].append([])
+        for x in range(100):
+            l[frame][y].append(random.randint(0, 50))
+
+image_seq = ImageSequence(l, sampling_rate=500 * pq.Hz, spatial_scale="m", units="V")
+
 def plot_roi(roi, shape):
     img = rand(120, 100)
     pir = np.array(roi.pixels_in_region()).T
@@ -22,17 +36,17 @@ def plot_roi(roi, shape):
     ax.add_artist(shape)
 
 
-roi = CircularRegionOfInterest(x=50.3, y=50.8, radius=30.2)
+roi = CircularRegionOfInterest(image_sequence=image_seq, x=50.3, y=50.8, radius=30.2)
 shape = plt.Circle(roi.centre, roi.radius, color="r", fill=False)
 plt.subplot(1, 3, 1)
 plot_roi(roi, shape)
 
-roi = RectangularRegionOfInterest(x=50.3, y=40.2, width=40.1, height=50.3)
+roi = RectangularRegionOfInterest(image_sequence=image_seq, x=50.3, y=40.2, width=40.1, height=50.3)
 shape = plt.Rectangle((roi.x - roi.width / 2.0, roi.y - roi.height / 2.0), roi.width, roi.height, color="r", fill=False)
 plt.subplot(1, 3, 2)
 plot_roi(roi, shape)
 
-roi = PolygonRegionOfInterest((20.3, 30.2), (80.7, 30.1), (55.2, 59.4))
+roi = PolygonRegionOfInterest(image_seq, (20.3, 30.2), (80.7, 30.1), (55.2, 59.4))
 shape = plt.Polygon(np.array(roi.vertices), closed=True, color="r", fill=False)
 plt.subplot(1, 3, 3)
 plot_roi(roi, shape)