Add MANIFEST.in and clean /JTM

.gitignore

@@ -131,4 +131,7 @@ dmypy.json
 # Folders to ignore
 matlab/
 lit/
+data/
+asano/
+img/
 

MANIFEST.in

@@ -0,0 +1 @@
+graft pysilsub 

bin/StimulationDevice_STLAB_demo.py

@@ -3,9 +3,9 @@
 
 # StimulationDevice class demonstration
 # =====================================
-# 
+#
 # Assumptions:
-# - This is intended to function as a generic device class for multiprimary stimulators. 
+# - This is intended to function as a generic device class for multiprimary stimulators.
 # - devices are additive
 # - calibration is stationary
 # - expect values as W/m2/nm
@@ -14,7 +14,8 @@
 
 
 import sys
-sys.path.insert(0, '../')
+
+sys.path.insert(0, "../")
 import random
 
 import matplotlib.pyplot as plt
@@ -25,8 +26,8 @@
 from silentsub.CIE import get_CIES026
 from silentsub import colorfunc
 
-sns.set_context('notebook')
-sns.set_style('whitegrid')
+sns.set_context("notebook")
+sns.set_style("whitegrid")
 
 
 # Load data with pandas -- this is our starting point
@@ -35,10 +36,12 @@
 # In[2]:
 
 
-spds = pd.read_csv('../data/S2_corrected_oo_spectra.csv', index_col=['led','intensity'])
-spds.index.rename(['Primary', 'Setting'], inplace=True)
+spds = pd.read_csv(
+    "../data/S2_corrected_oo_spectra.csv", index_col=["led", "intensity"]
+)
+spds.index.rename(["Primary", "Setting"], inplace=True)
 spds.columns = pd.Int64Index(spds.columns.astype(int))
-spds.columns.name = 'Wavelength'
+spds.columns.name = "Wavelength"
 spds = spds.sort_index()
 spds
 
@@ -50,15 +53,22 @@
 
 
 # list of colors for the primaries
-colors = ['blueviolet', 'royalblue', 'darkblue', 'blue', 'cyan', 
-          'green', 'lime', 'orange', 'red', 'darkred']
+colors = [
+    "blueviolet",
+    "royalblue",
+    "darkblue",
+    "blue",
+    "cyan",
+    "green",
+    "lime",
+    "orange",
+    "red",
+    "darkred",
+]
 
 # instantiate the class
 device = StimulationDevice(
-    resolutions=[4095]*10,
-    colors=colors,
-    spds=spds,
-    spd_binwidth=1
+    resolutions=[4095] * 10, colors=colors, spds=spds, spd_binwidth=1
 )
 
 
@@ -87,11 +97,9 @@
 
 
 primary_spd = device.predict_primary_spd(
-    primary=7, 
-    setting=.5, 
-    name='Primary 7 (half power)'
+    primary=7, setting=0.5, name="Primary 7 (half power)"
 )
-primary_spd.plot(legend=True, ylabel='W/m$^2$/nm', color=device.colors[7]);
+primary_spd.plot(legend=True, ylabel="W/m$^2$/nm", color=device.colors[7])
 
 
 # Predict output for random device settings
@@ -100,19 +108,21 @@
 # In[7]:
 
 
-settings = [random.randrange(s) for s in device.resolutions] # Using a list of integers
-device_spd = device.predict_multiprimary_spd(settings, 'Random SPD')
-device_spd.plot(legend=True, ylabel='W/m$^2$/nm');
-print(f'Predicted output for device settings: {settings}')
+settings = [
+    random.randrange(s) for s in device.resolutions
+]  # Using a list of integers
+device_spd = device.predict_multiprimary_spd(settings, "Random SPD")
+device_spd.plot(legend=True, ylabel="W/m$^2$/nm")
+print(f"Predicted output for device settings: {settings}")
 
 
 # In[8]:
 
 
-weights = device.settings_to_weights(settings) # Convert settings to float
-device_spd = device.predict_multiprimary_spd(weights, 'Random SPD')
-device_spd.plot(legend=True, ylabel='W/m$^2$/nm');
-print(f'Predicted output for device settings: {weights}')
+weights = device.settings_to_weights(settings)  # Convert settings to float
+device_spd = device.predict_multiprimary_spd(weights, "Random SPD")
+device_spd.plot(legend=True, ylabel="W/m$^2$/nm")
+print(f"Predicted output for device settings: {weights}")
 
 
 # Predict *a*-opic irradiances for a list of device settings and plot with nice colours
@@ -123,7 +133,7 @@
 
 device_ao = device.predict_multiprimary_aopic(settings)
 ao_colors = list(device.aopic_colors.values())
-device_ao.plot(kind='bar', color=ao_colors, ylabel='W/m$^2$');
+device_ao.plot(kind="bar", color=ao_colors, ylabel="W/m$^2$")
 
 
 # Convert settings to weights and weights to settings
@@ -147,34 +157,34 @@
 # In[12]:
 
 
-xy = [.3127, .3290]  # D65
-luminance = 600.  # Lux
+xy = [0.3127, 0.3290]  # D65
+luminance = 600.0  # Lux
 res = device.find_settings_xyY(
-    xy=xy, 
+    xy=xy,
     luminance=luminance,
     tollerance=1e-6,
     plot_solution=True,
-    verbose=True
+    verbose=True,
 )
 
 
 # In[13]:
 import numpy as np
+
 bg = device.predict_multiprimary_spd(
-    [.2 for val in range(10)],
-    'background',
-    nosum=True)
+    [0.2 for val in range(10)], "background", nosum=True
+)
 
 sss = get_CIES026()
 mat = bg.T.dot(sss)
 pinv_mat = np.linalg.pinv(mat)
 mod = np.dot(pinv_mat.T, np.array([0, 0, 0, 0, 0]))
-device.predict_multiprimary_spd([.5 for val in range(10)] + mod, 'mod').plot(legend=True); 
-device.predict_multiprimary_spd([.5 for val in range(10)], 'notmod').plot(legend=True);
+device.predict_multiprimary_spd([0.5 for val in range(10)] + mod, "mod").plot(
+    legend=True
+)
+device.predict_multiprimary_spd([0.5 for val in range(10)], "notmod").plot(
+    legend=True
+)
 
 
 # In[ ]:
-
-
-
-

bin/config_BCGAR_8_bit_linear.py

@@ -11,31 +11,35 @@
 
 # Configure device
 RESOLUTIONS = [255] * 5
-COLORS = ['blue', 'cyan', 'green', 'orange', 'red']
-CALIBRATION_FPATH= '/Users/jtm545/Projects/PySilSub/data/BCGAR_5_Primary_8_bit_linear.csv'
-CALIBRATION_UNITS = 'W/m$^2$/nm'
-NAME = 'BCGAR (8-bit, linear)'
-JSON_NAME = 'BCGAR'
+COLORS = ["blue", "cyan", "green", "orange", "red"]
+CALIBRATION_FPATH = (
+    "/Users/jtm545/Projects/PySilSub/data/BCGAR_5_Primary_8_bit_linear.csv"
+)
+CALIBRATION_UNITS = "W/m$^2$/nm"
+NAME = "BCGAR (8-bit, linear)"
+JSON_NAME = "BCGAR"
 WAVELENGTHS = [380, 781, 1]
-NOTES = ('An artificial 8-bit linear calibration based on the maximum output '
-         + 'of 5 STLAB channels.')
+NOTES = (
+    "An artificial 8-bit linear calibration based on the maximum output "
+    + "of 5 STLAB channels."
+)
 
 
 def device_config():
-    
+
     config = {
-        'calibration_fpath': CALIBRATION_FPATH,
-        'calibration_units': CALIBRATION_UNITS,
-        'name': NAME,
-        'json_name': JSON_NAME,
-        'wavelengths': WAVELENGTHS,
-        'colors': COLORS,
-        'resolutions': RESOLUTIONS,
-        'notes': NOTES
-        }
-    
-    json.dump(config, open(f'../data/{JSON_NAME}.json', 'w'))
-    
-
-if __name__ == '__main__':
-    device_config()
+        "calibration_fpath": CALIBRATION_FPATH,
+        "calibration_units": CALIBRATION_UNITS,
+        "name": NAME,
+        "json_name": JSON_NAME,
+        "wavelengths": WAVELENGTHS,
+        "colors": COLORS,
+        "resolutions": RESOLUTIONS,
+        "notes": NOTES,
+    }
+
+    json.dump(config, open(f"../data/{JSON_NAME}.json", "w"))
+
+
+if __name__ == "__main__":
+    device_config()

bin/config_OneLight.py

@@ -16,15 +16,27 @@
 
 # Configure device
 RESOLUTIONS = [256] * 56
-COLORS = list(sns.color_palette('Spectral', n_colors=56))[::-1]
+COLORS = list(sns.color_palette("Spectral", n_colors=56))[::-1]
 # Absolute file path to permenant location of calibration file
-CALIBRATION_FPATH = '/Users/jtm545/Projects/PySilSub/data/oneLight_artifical.csv'
-CALIBRATION_UNITS = 'W/$m^2$/s/nm'
-NAME = 'OneLight'
-JSON_NAME = 'OneLight'
+CALIBRATION_FPATH = (
+    "/Users/jtm545/Projects/PySilSub/data/oneLight_artifical.csv"
+)
+CALIBRATION_UNITS = "W/$m^2$/s/nm"
+NAME = "OneLight"
+JSON_NAME = "OneLight"
 WAVELENGTHS = [380, 781, 2]
-NOTES = ('Device used in Spitschan et al. papers. Highly linear with 52 '
-         + 'primaries. Perfectly linear in this dataset.')
+NOTES = (
+    "OneLight VISX Spectra, digital light synthesis engine used in Spitschan "
+    + "et al. papers. Highly linear with 52 narrow-band (16 nm FWHM) "
+    + "primaries and the capacity to modulate between spectra at 256 Hz. "
+    + "Reinvented from original measurements here as a perfectly linear "
+    + "device with 8-bit channel resolution. For further details, see "
+    + "Spitschan, M., Aguirre, G. K., & Brainard, D. H. (2015). Selective "
+    + "stimulation of penumbral cones reveals perception in the shadow of "
+    + "retinal blood vessels. PLoS ONE, 10(4), 1–22. "
+    + "https://doi.org/10.1371/journal.pone.0124328"
+)
+
 
 
 def device_config():
@@ -36,20 +48,20 @@ def device_config():
     None.
 
     """
-    
+
     config = {
-        'calibration_fpath': CALIBRATION_FPATH,
-        'calibration_units':CALIBRATION_UNITS,
-        'name': NAME,
-        'json_name': JSON_NAME,
-        'wavelengths': WAVELENGTHS,
-        'colors': COLORS,
-        'resolutions': RESOLUTIONS,
-        'notes': NOTES
-        }
-    
-    json.dump(config, open(f'../data/{JSON_NAME}.json', 'w'))
-    
+        "calibration_fpath": CALIBRATION_FPATH,
+        "calibration_units": CALIBRATION_UNITS,
+        "name": NAME,
+        "json_name": JSON_NAME,
+        "wavelengths": WAVELENGTHS,
+        "colors": COLORS,
+        "resolutions": RESOLUTIONS,
+        "notes": NOTES,
+    }
+
+    json.dump(config, open(f"../data/{JSON_NAME}.json", "w"))
+
 
-if __name__ == '__main__':
-    device_config()
+if __name__ == "__main__":
+    device_config()