Change location of channel density plots

NeuroML · Sep 19, 2023 · c90cd3a · c90cd3a
1 parent e4c7963
commit c90cd3a
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Showing 4 changed files with 20 additions and 17 deletions.
diff --git a/.gitignore b/.gitignore
@@ -164,3 +164,4 @@ arm64
 /tests/plot/test_schematic_plot_2d_test_cell_nml_xy.png
 /tests/plot/test_schematic_plot_2d_test_cell_nml_xz.png
 /tests/plot/test_schematic_plot_2d_test_cell_nml_yz.png
+/tests/analysis/*png
diff --git a/examples/LeakConductance.mod b/examples/LeakConductance.mod
@@ -18,9 +18,7 @@ NEURON {
     RANGE i__LeakConductance : a copy of the variable for current which makes it easier to access from outside the mod file
     RANGE gmax                              : Will be changed when ion channel mechanism placed on cell!
     RANGE conductance                       : parameter
-
     RANGE g                                 : exposure
-
     RANGE fopen                             : exposure
     RANGE conductanceScale                  : derived variable
     RANGE fopen0                            : derived variable
@@ -36,11 +34,13 @@ UNITS {
     (mV) = (millivolt)
     (mS) = (millisiemens)
     (uS) = (microsiemens)
+    (nF) = (nanofarad)
     (molar) = (1/liter)
     (kHz) = (kilohertz)
     (mM) = (millimolar)
     (um) = (micrometer)
     (umol) = (micromole)
+    (pC) = (picocoulomb)
     (S) = (siemens)
 
 }
@@ -49,7 +49,7 @@ PARAMETER {
 
     gmax = 0  (S/cm2)                       : Will be changed when ion channel mechanism placed on cell!
 
-    conductance = 1.0E-5 (uS)
+    conductance = 1.0E-5 (uS)              : was: 1.0E-11 (conductance)
 }
 
 ASSIGNED {
@@ -62,14 +62,10 @@ ASSIGNED {
     i (mA/cm2)
     i__LeakConductance (mA/cm2)
 
-
-    conductanceScale                       : derived variable
-
-    fopen0                                 : derived variable
-
-    fopen                                  : derived variable
-
-    g (uS)                                 : derived variable
+    conductanceScale                        : derived variable
+    fopen0                                  : derived variable
+    fopen                                   : derived variable
+    g (uS)                                  : derived variable
 
 }
 

diff --git a/pyneuroml/analysis/ChannelDensityPlot.py b/pyneuroml/analysis/ChannelDensityPlot.py
@@ -564,6 +564,7 @@ def plot_channel_densities(
     show_plots_already: bool = True,
     morph_plot_type: str = "constant",
     morph_min_width: float = 2.0,
+    target_directory=None
 ):
     """Plot channel densities on a Cell on morphology plots.
 
@@ -603,6 +604,8 @@ def plot_channel_densities(
     :type colormap_name: str
     :returns: None
     """
+    tgt_dir = target_directory+'/' if target_directory else './'
+
     if channel_density_ids is not None and ion_channels is not None:
         raise ValueError(
             "Only one of channel_density_ids or ions channels may be provided"
@@ -685,7 +688,7 @@ def plot_channel_densities(
                         min_width=morph_min_width,
                         overlay_data=data,
                         overlay_data_label="(S/m2)",
-                        save_to_file=f"{cell.id}_{cd.id}.cd.png",
+                        save_to_file=f"{tgt_dir}{cell.id}_{cd.id}.cd.png",
                         datamin=ymin,
                         plane2d=plane2d,
                         nogui=not show_plots_already,
@@ -710,7 +713,7 @@ def plot_channel_densities(
                             title_above_plot=True,
                             xaxis="Distance from soma (um)",
                             yaxis="g density (S/m2)",
-                            save_figure_to=f"{cell.id}_{cd.id}_cd_vs_dist.png",
+                            save_figure_to=f"{tgt_dir}{cell.id}_{cd.id}_cd_vs_dist.png",
                             show_plot_already=show_plots_already,
                             linestyles=[" "],
                             linewidths=["0"],
@@ -786,7 +789,7 @@ def plot_channel_densities(
                     min_width=morph_min_width,
                     overlay_data=data,
                     overlay_data_label="(S/m2)",
-                    save_to_file=f"{cell.id}_{ion_channel}.ion.png",
+                    save_to_file=f"{tgt_dir}{cell.id}_{ion_channel}.ion.png",
                     datamin=ymin,
                     plane2d=plane2d,
                     nogui=not show_plots_already,
@@ -811,7 +814,7 @@ def plot_channel_densities(
                         title_above_plot=True,
                         xaxis="Distance from soma (um)",
                         yaxis="g density (S/m2)",
-                        save_figure_to=f"{cell.id}_{ion_channel}_ion_vs_dist.png",
+                        save_figure_to=f"{tgt_dir}{cell.id}_{ion_channel}_ion_vs_dist.png",
                         show_plot_already=show_plots_already,
                         linestyles=[" "],
                         linewidths=["0"],

diff --git a/tests/analysis/test_channel_density_plots.py b/tests/analysis/test_channel_density_plots.py
@@ -75,10 +75,13 @@ def test_plot_channel_densities(self):
             channel_density_ids=["Ih_apical", "Ih_somatic", "Ih_basal", "Ih"],
             distance_plots=True,
             show_plots_already=False,
+            target_directory='tests/analysis'
         )
         plot_channel_densities(
-            cell, ion_channels=["Ih"], distance_plots=True, show_plots_already=False
+            cell, ion_channels=["Ih"], distance_plots=True, show_plots_already=False,
+            target_directory='tests/analysis'
         )
         # no channel densities or ion channels, so generate for all ion
         # channels
-        plot_channel_densities(cell, distance_plots=True, show_plots_already=False)
+        plot_channel_densities(cell, distance_plots=True, show_plots_already=False,
+            target_directory='tests/analysis')