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Multiple plots (#294)
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* handling plotting of multiple different plots

* updating readme

* addressing test faiulures
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@K20shores
K20shores authored Dec 19, 2024
1 parent 1d7fe7c commit ee8950a
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8 changes: 8 additions & 0 deletions README.md
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Expand Up @@ -78,6 +78,14 @@ Some basic plots can be made to show concentrations throughout the simulation
music_box -e Chapman -o output.csv --plot O1D
```

You can also make multiple plots by specifying groupings of species

```
music_box -e TS1 --plot O3 --plot PAN,HF
```

Note that the windows may overlap each other

### gnuplot
If you want ascii plots (maybe you're running over ssh and can't view a graphical window), you can set
the plot tool to gnuplo (`--plot-tool gnuplot`) to view some output
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4 changes: 2 additions & 2 deletions src/acom_music_box/examples/configs/ts1/initial_conditions.csv
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@@ -1,2 +1,2 @@
temperature [K],pressure [Pa],ALKNIT [mol m-3],BCARY [mol m-3],BENZENE [mol m-3],BIGALD [mol m-3],BIGALD1 [mol m-3],BIGALD2 [mol m-3],BIGALD3 [mol m-3],BIGALD4 [mol m-3],BIGALK [mol m-3],BIGENE [mol m-3],C2H2 [mol m-3],C2H4 [mol m-3],C2H5OH [mol m-3],C2H6 [mol m-3],C3H6 [mol m-3],C3H8 [mol m-3],CH2O [mol m-3],CH3CHO [mol m-3],CH3CN [mol m-3],CH3COCH3 [mol m-3],CH3COCHO [mol m-3],CH3COOH [mol m-3],CH3OH [mol m-3],CH3OOH [mol m-3],CH4 [mol m-3],CHBR3 [mol m-3],CO [mol m-3],CRESOL [mol m-3],DMS [mol m-3],GLYOXAL [mol m-3],H2O [mol m-3],H2O2 [mol m-3],HCN [mol m-3],HCOOH [mol m-3],HNO3 [mol m-3],HO2 [mol m-3],HO2NO2 [mol m-3],HONITR [mol m-3],HYAC [mol m-3],ISOP [mol m-3],ISOPNITA [mol m-3],ISOPNITB [mol m-3],MACR [mol m-3],MEK [mol m-3],MPAN [mol m-3],MTERP [mol m-3],MVK [mol m-3],N2O [mol m-3],N2O5 [mol m-3],NH3 [mol m-3],NH4 [mol m-3],NO [mol m-3],NO2 [mol m-3],NO3 [mol m-3],NOA [mol m-3],O3 [mol m-3],OH [mol m-3],ONITR [mol m-3],PAN [mol m-3],PBZNIT [mol m-3],PHENOL [mol m-3],SO2 [mol m-3],TERPNIT [mol m-3],TOLUENE [mol m-3],XYLENES [mol m-3],soa1_a1 [mol m-3],soa1_a2 [mol m-3],soa2_a1 [mol m-3],soa2_a2 [mol m-3],soa3_a1 [mol m-3],soa3_a2 [mol m-3],soa4_a1 [mol m-3],soa4_a2 [mol m-3],soa5_a1 [mol m-3],soa5_a2 [mol m-3],N2 [mol m-3],O2 [mol m-3],Ar [mol m-3]
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3 changes: 1 addition & 2 deletions src/acom_music_box/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ def parse_arguments():
parser.add_argument(
'--plot',
type=str,
action='append',
help='Plot a comma-separated list of species if gnuplot is available (e.g., CONC.A,CONC.B).'
)
parser.add_argument(
Expand Down Expand Up @@ -114,8 +115,6 @@ def main():
else:
musicBoxConfigFile = args.config

plot_species_list = args.plot.split(',') if args.plot else None

if not musicBoxConfigFile:
error = "Configuration file is required."
logger.error(error)
Expand Down
111 changes: 59 additions & 52 deletions src/acom_music_box/plot_output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@ class PlotOutput:
The DataFrame to be plotted.
args : argparse.Namespace
Command-line arguments or configurations specifying plot options.
species_list : list
A list of species to plot.
species_list : list of lists
A list of lists, where each sublist contains species to be plotted in a separate window.
Examples
--------
Expand All @@ -35,7 +35,7 @@ class PlotOutput:
... 'CONC.B.mol m-3': [4, 5, 6],
... 'CONC.C.mol m-3': [7, 8, 9]
... })
>>> args = Namespace(plot='CONC.A,CONC.B', plot_tool='matplotlib')
>>> args = Namespace(plot=['CONC.A,CONC.B'], plot_tool='matplotlib')
>>> plot_output = PlotOutput(df, args)
>>> plot_output.plot()
"""
Expand All @@ -54,7 +54,10 @@ def __init__(self, df, args):

self.df = df.copy(deep=True)
self.args = args
self.species_list = self._format_species_list(self.args.plot.split(',') if self.args.plot else None)
if self.args.plot:
self.species_list = [self._format_species_list(group.split(',')) for group in self.args.plot]
else:
self.species_list = None

def _format_species_list(self, species_list):
"""
Expand Down Expand Up @@ -90,64 +93,68 @@ def _plot_with_gnuplot(self):
Plot the specified species using gnuplot.
"""
# Prepare columns and data for plotting
columns = ['time'] + self.species_list
data_to_plot = self.df[columns]

data_csv = data_to_plot.to_csv(index=False)

try:
with tempfile.NamedTemporaryFile(suffix='.csv', mode='w+', delete=True) as data_file:
data_file.write(data_csv)
data_file.flush()
data_file_path = data_file.name

plot_commands = ',\n\t'.join(
f"'{data_file_path}' using 1:{i+2} with lines title '{species}'" for i,
species in enumerate(self.species_list))

gnuplot_command = f"""
set datafile separator ",";
set terminal dumb size 120,25;
set xlabel 'Time';
set ylabel 'Value';
set title 'Time vs Species';
plot {plot_commands}
"""

subprocess.run(['gnuplot', '-e', gnuplot_command], check=True)
except FileNotFoundError as e:
logging.critical("gnuplot is not installed. Skipping plotting.")
raise e
except subprocess.CalledProcessError as e:
logging.error(f"Error occurred while plotting: {e}")
raise e
if not self.species_list:
return;
for species_group in self.species_list:
columns = ['time'] + species_group
data_to_plot = self.df[columns]

data_csv = data_to_plot.to_csv(index=False)

try:
with tempfile.NamedTemporaryFile(suffix='.csv', mode='w+', delete=True) as data_file:
data_file.write(data_csv)
data_file.flush()
data_file_path = data_file.name

plot_commands = ',\n\t'.join(
f"'{data_file_path}' using 1:{i+2} with lines title '{species}'" for i,
species in enumerate(species_group))

gnuplot_command = f"""
set datafile separator ",";
set terminal dumb size 120,25;
set xlabel 'Time';
set ylabel 'Value';
set title 'Time vs Species';
plot {plot_commands}
"""

subprocess.run(['gnuplot', '-e', gnuplot_command], check=True)
except FileNotFoundError as e:
logging.critical("gnuplot is not installed. Skipping plotting.")
raise e
except subprocess.CalledProcessError as e:
logging.error(f"Error occurred while plotting: {e}")
raise e

def _plot_with_matplotlib(self):
"""
Plot the specified species using matplotlib.
"""
if not self.species_list:
return;
for species_group in self.species_list:
indexed = self.df.set_index('time')
fig, ax = plt.subplots()
indexed[species_group].plot(ax=ax)

indexed = self.df.set_index('time')

fig, ax = plt.subplots()
indexed[self.species_list].plot(ax=ax)

ax.set(xlabel='Time [s]', ylabel='Concentration [mol m-3]', title='Time vs Species')
ax.set(xlabel='Time [s]', ylabel='Concentration [mol m-3]', title='Time vs Species')

ax.spines[:].set_visible(False)
ax.spines['left'].set_visible(True)
ax.spines['bottom'].set_visible(True)
ax.spines[:].set_visible(False)
ax.spines['left'].set_visible(True)
ax.spines['bottom'].set_visible(True)

ax.grid(alpha=0.5)
ax.legend()
ax.grid(alpha=0.5)
ax.legend()

# Enable interactive data cursors with hover functionality
cursor = mplcursors.cursor(hover=True)
# Enable interactive data cursors with hover functionality
cursor = mplcursors.cursor(hover=True)

# Customize the annotation format
@cursor.connect("add")
def on_add(sel):
sel.annotation.set_text(f'Time: {sel.target[0]:.2f}\nConcentration: {sel.target[1]:1.2e}')
# Customize the annotation format
@cursor.connect("add")
def on_add(sel):
sel.annotation.set_text(f'Time: {sel.target[0]:.2f}\nConcentration: {sel.target[1]:1.2e}')

plt.show()

Expand Down
24 changes: 19 additions & 5 deletions tests/unit/test_plot_output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,17 +21,17 @@ def setUp(self):
})

def test_format_species_list(self):
args = Namespace(plot='A,B', plot_tool='matplotlib')
args = Namespace(plot=['A', 'B'], plot_tool='matplotlib')
plot_output = PlotOutput(self.df, args)
expected_list = ['CONC.A', 'CONC.B']
expected_list = [['CONC.A'], ['CONC.B']]
self.assertEqual(plot_output.species_list, expected_list)

args = Namespace(plot='CONC.A,CONC.B', plot_tool='matplotlib')
args = Namespace(plot=['CONC.A', 'CONC.B'], plot_tool='matplotlib')
plot_output = PlotOutput(self.df, args)
self.assertEqual(plot_output.species_list, expected_list)

def test_plot_with_gnuplot(self):
args = Namespace(plot='A,B', plot_tool='gnuplot')
args = Namespace(plot=['A', 'B'], plot_tool='gnuplot')
plot_output = PlotOutput(self.df, args)
if shutil.which('gnuplot') is None:
with self.assertRaises(FileNotFoundError):
Expand All @@ -40,7 +40,21 @@ def test_plot_with_gnuplot(self):
plot_output.plot()

def test_plot_with_matplotlib(self):
args = Namespace(plot='A,B', plot_tool='matplotlib')
args = Namespace(plot=['A', 'B'], plot_tool='matplotlib')
plot_output = PlotOutput(self.df, args)
plot_output.plot()

def test_multiple_groups_with_gnuplot(self):
args = Namespace(plot=['A,B', 'C'], plot_tool='gnuplot')
plot_output = PlotOutput(self.df, args)
if shutil.which('gnuplot') is None:
with self.assertRaises(FileNotFoundError):
plot_output.plot()
else:
plot_output.plot()

def test_multiple_groups_with_matplotlib(self):
args = Namespace(plot=['A,B', 'C'], plot_tool='matplotlib')
plot_output = PlotOutput(self.df, args)
plot_output.plot()

Expand Down

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