Merge pull request #221 from NeuroML/experimental

A few minor changes and bugfix for 2d plotting

Author: sanjayankur31

.gitignore

@@ -151,5 +151,7 @@ examples/results/*.dat
 /tests/iv_izh2007RS0.net.nml
 /tests/leak_chan.channel.nml
 /tests/test_cell_analysis.cell.nml
-
+arm64
 *.neux
+/test_*plot*png
+/examples/plot.py

pyneuroml/plot/Plot.py

@@ -177,15 +177,14 @@ def generate_plot(
         label = "" if not labels else labels[i]
         marker = None if not markers else markers[i]
         linewidth = 1 if not linewidths else linewidths[i]
-        markersize = 6 if not markersizes else markersizes[i]
+        markersize = None if not markersizes else markersizes[i]
 
         if colors:
             plt.plot(
                 xvalues[i],
                 yvalues[i],
-                "o",
-                color=colors[i],
                 marker=marker,
+                color=colors[i],
                 markersize=markersize,
                 linestyle=linestyle,
                 linewidth=linewidth,
@@ -195,7 +194,6 @@ def generate_plot(
             plt.plot(
                 xvalues[i],
                 yvalues[i],
-                "o",
                 marker=marker,
                 markersize=markersize,
                 linestyle=linestyle,
@@ -385,7 +383,7 @@ def generate_interactive_plot(
         raise ValueError("labels not provided correctly")
 
     if not markersizes:
-        markersizes = len(xvalues) * [6.0]
+        markersizes = len(xvalues) * [6]
     if not markers:
         markers = len(xvalues) * [0]
     if not linestyles:

pyneuroml/plot/PlotSpikes.py

@@ -12,9 +12,13 @@
 
 logger = logging.getLogger(__name__)
 
+FORMAT_ID_T = "id_t"
+FORMAT_ID_TIME_NEST_DAT = "id_t_nest_dat"
+FORMAT_T_ID = "t_id"
+
 
 DEFAULTS = {
-    "format": "id_t",
+    "format": FORMAT_ID_T,
     "rates": False,
     "save_spike_plot_to": None,
     "rate_window": 50,
@@ -74,8 +78,9 @@ def process_args():
         metavar="<format>",
         default=DEFAULTS["format"],
         help="How the spiketimes are represented on each line of file: \n"
-        + "id_t: id of cell, space(s) / tab(s), time of spike (default);\n"
-        + "t_id: time of spike, space(s) / tab(s), id of cell;\n"
+        + "%s: id of cell, space(s) / tab(s), time of spike (default);\n"%FORMAT_ID_T
+        + "%s: id of cell, space(s) / tab(s), time of spike, allowing NEST dat file comments/metadata;\n"%FORMAT_ID_TIME_NEST_DAT
+        + "%s: time of spike, space(s) / tab(s), id of cell;\n"%FORMAT_T_ID
         + "sonata: SONATA format HDF5 file containing spike times",
     )
 
@@ -288,10 +293,10 @@ def run(a=None, **kwargs):
             ids_in_file[name] = []
 
             for line in spikes_file:
-                if not line.startswith("#"):
-                    if a.format == "id_t":
+                if not line.startswith("#") and not (line.startswith("sender") and a.format == FORMAT_ID_TIME_NEST_DAT):
+                    if a.format == FORMAT_ID_T or a.format == FORMAT_ID_TIME_NEST_DAT:
                         [id, t] = line.split()
-                    elif a.format == "t_id":
+                    elif a.format == FORMAT_T_ID:
                         [t, id] = line.split()
                     id_shifted = offset_id + int(float(id))
                     max_id = max(max_id, id_shifted)

setup.py

@@ -92,7 +92,6 @@
     long_description=open("README.md").read(),
     long_description_content_type="text/markdown",
     install_requires=[
-        "argparse",
         "pylems>=0.5.7",
         "airspeed>=0.5.5",
         "neuromllite>=0.4.1",  # sets dependency for libNeuroML also

test-ghactions.sh

@@ -1,6 +1,6 @@
 set -e
 
-python setup.py install
+pip install .
 
 echo
 echo "################################################"