From f7a6fc8c469603305cec12e5e0f136c85c72e11d Mon Sep 17 00:00:00 2001
From: Brent Huisman <brenthuisman@users.noreply.github.com>
Date: Mon, 16 Aug 2021 17:57:28 +0200
Subject: [PATCH] Update Python examples to work with latest Pandas+Seaborn
(#1625)
Latest Pandas versions required unique indices, breaking the plotting in the python examples.
---
python/example/network_ring.py | 2 +-
python/example/network_ring_mpi.py | 2 +-
python/example/network_ring_mpi_plot.py | 4 ++--
python/example/single_cell_detailed.py | 6 +++---
python/example/single_cell_detailed_recipe.py | 5 +++--
python/example/single_cell_model.py | 6 ++----
python/example/single_cell_nml.py | 2 +-
python/example/single_cell_recipe.py | 2 +-
python/example/single_cell_swc.py | 2 +-
9 files changed, 15 insertions(+), 16 deletions(-)
diff --git a/python/example/network_ring.py b/python/example/network_ring.py
index c1c6a07b..46c6ada3 100755
--- a/python/example/network_ring.py
+++ b/python/example/network_ring.py
@@ -137,5 +137,5 @@ for gid in range(ncells):
samples, meta = sim.samples(handles[gid])[0]
df_list.append(pandas.DataFrame({'t/ms': samples[:, 0], 'U/mV': samples[:, 1], 'Cell': f"cell {gid}"}))
-df = pandas.concat(df_list)
+df = pandas.concat(df_list,ignore_index=True)
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",hue="Cell",ci=None).savefig('network_ring_result.svg')
diff --git a/python/example/network_ring_mpi.py b/python/example/network_ring_mpi.py
index 51bde9d4..52e88aec 100644
--- a/python/example/network_ring_mpi.py
+++ b/python/example/network_ring_mpi.py
@@ -143,5 +143,5 @@ for gid in range(ncells):
df_list.append(pandas.DataFrame({'t/ms': samples[:, 0], 'U/mV': samples[:, 1], 'Cell': f"cell {gid}"}))
if len(df_list):
- df = pandas.concat(df_list)
+ df = pandas.concat(df_list,ignore_index=True)
df.to_csv(f"result_mpi_{context.rank}.csv", float_format='%g')
diff --git a/python/example/network_ring_mpi_plot.py b/python/example/network_ring_mpi_plot.py
index c5ec346c..5f54baef 100644
--- a/python/example/network_ring_mpi_plot.py
+++ b/python/example/network_ring_mpi_plot.py
@@ -10,5 +10,5 @@ df_list = []
for result in results:
df_list.append(pandas.read_csv(result))
-df = pandas.concat(df_list)
-seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",hue="Cell",ci=None).savefig('mpi_result.svg')
\ No newline at end of file
+df = pandas.concat(df_list,ignore_index=True)
+seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",hue="Cell",ci=None).savefig('mpi_result.svg')
diff --git a/python/example/single_cell_detailed.py b/python/example/single_cell_detailed.py
index b19627f9..0ff3af50 100755
--- a/python/example/single_cell_detailed.py
+++ b/python/example/single_cell_detailed.py
@@ -118,8 +118,8 @@ for s in model.spikes:
# (10) Plot the voltages
-df = pandas.DataFrame()
+df_list = []
for t in model.traces:
- df=df.append(pandas.DataFrame({'t/ms': t.time, 'U/mV': t.value, 'Location': str(t.location), 'Variable': t.variable}))
-
+ df_list.append(pandas.DataFrame({'t/ms': t.time, 'U/mV': t.value, 'Location': str(t.location), 'Variable': t.variable}))
+df = pandas.concat(df_list,ignore_index=True)
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",hue="Location",col="Variable",ci=None).savefig('single_cell_detailed_result.svg')
diff --git a/python/example/single_cell_detailed_recipe.py b/python/example/single_cell_detailed_recipe.py
index 281da877..d9275e8d 100644
--- a/python/example/single_cell_detailed_recipe.py
+++ b/python/example/single_cell_detailed_recipe.py
@@ -182,7 +182,8 @@ for d, m in sim.samples(handle):
data.append(d)
meta.append(m)
-df = pandas.DataFrame()
+df_list = []
for i in range(len(data)):
- df = df.append(pandas.DataFrame({'t/ms': data[i][:, 0], 'U/mV': data[i][:, 1], 'Location': str(meta[i]), 'Variable':'voltage'}))
+ df_list.append(pandas.DataFrame({'t/ms': data[i][:, 0], 'U/mV': data[i][:, 1], 'Location': str(meta[i]), 'Variable':'voltage'}))
+df = pandas.concat(df_list,ignore_index=True)
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",hue="Location",col="Variable",ci=None).savefig('single_cell_recipe_result.svg')
diff --git a/python/example/single_cell_model.py b/python/example/single_cell_model.py
index e8e461c4..a21445d3 100755
--- a/python/example/single_cell_model.py
+++ b/python/example/single_cell_model.py
@@ -4,8 +4,6 @@
import arbor
import pandas, seaborn # You may have to pip install these.
-print(arbor.__config__)
-
# (1) Create a morphology with a single (cylindrical) segment of length=diameter=6 μm
tree = arbor.segment_tree()
tree.append(arbor.mnpos, arbor.mpoint(-3, 0, 0, 3), arbor.mpoint(3, 0, 0, 3), tag=1)
@@ -41,11 +39,11 @@ if len(m.spikes)>0:
else:
print('no spikes')
-# (8) Plot the recorded voltages over time.
+# (9) Plot the recorded voltages over time.
print("Plotting results ...")
seaborn.set_theme() # Apply some styling to the plot
df = pandas.DataFrame({'t/ms': m.traces[0].time, 'U/mV': m.traces[0].value})
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",ci=None).savefig('single_cell_model_result.svg')
-# (9) Optionally, you can store your results for later processing.
+# (10) Optionally, you can store your results for later processing.
df.to_csv('single_cell_model_result.csv', float_format='%g')
diff --git a/python/example/single_cell_nml.py b/python/example/single_cell_nml.py
index 7c5920bc..d582b36b 100755
--- a/python/example/single_cell_nml.py
+++ b/python/example/single_cell_nml.py
@@ -103,6 +103,6 @@ df_list = []
for t in m.traces:
df_list.append(pandas.DataFrame({'t/ms': t.time, 'U/mV': t.value, 'Location': str(t.location), "Variable": t.variable}))
-df = pandas.concat(df_list)
+df = pandas.concat(df_list,ignore_index=True)
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",hue="Location",col="Variable",ci=None).savefig('single_cell_nml.svg')
diff --git a/python/example/single_cell_recipe.py b/python/example/single_cell_recipe.py
index 01af5d46..193e258a 100644
--- a/python/example/single_cell_recipe.py
+++ b/python/example/single_cell_recipe.py
@@ -87,7 +87,7 @@ else:
print('no spikes')
print("Plotting results ...")
-seaborn.set_theme() # Apply some styling to the plot
+
df = pandas.DataFrame({'t/ms': data[:, 0], 'U/mV': data[:, 1]})
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV", ci=None).savefig('single_cell_recipe_result.svg')
diff --git a/python/example/single_cell_swc.py b/python/example/single_cell_swc.py
index 525d90e8..2090f16d 100755
--- a/python/example/single_cell_swc.py
+++ b/python/example/single_cell_swc.py
@@ -95,6 +95,6 @@ df_list = []
for t in m.traces:
df_list.append(pandas.DataFrame({'t/ms': t.time, 'U/mV': t.value, 'Location': str(t.location), "Variable": t.variable}))
-df = pandas.concat(df_list)
+df = pandas.concat(df_list,ignore_index=True)
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",hue="Location",col="Variable",ci=None).savefig('single_cell_swc.svg')
--
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