Use on off indices from on off steps, plot all

- On off indices obtained from on off steps stimulus from Dimos, save them into full field
flicker .npz file and retrieve in on_off_plotter
- Plot all on off graphs together in a loop

checkerflicker_analysis_dimos.py

@@ -10,7 +10,6 @@
 import sys
 import numpy as np
 from collections import Counter
-import matplotlib.pyplot as plt
 import scipy.io
 # Custom packages
 try:
@@ -22,7 +21,7 @@
     import lnp
 
 main_dir = '/Users/ycan/Documents/official/gottingen/lab rotations/\
-LR3 Gollisch/data/Experiments/Mouse/2016_10_21/'
+LR3 Gollisch/data/Experiments/Mouse/2017_01_31/'
 
 cells_classified = main_dir+'clusters.mat'
 
@@ -104,7 +103,6 @@
     peak, onoffindex = lnpc.onoffindex(v[:, 0], bins[1],
                                        spike_counts_in_bins[1])
 
-#%%
     np.savez(save_path,
              sta_unscaled=sta_unscaled,
              sta_weighted=sta_weighted,

fff_analysis_dimos.py

@@ -12,7 +12,6 @@
 import sys
 import numpy as np
 from collections import Counter
-import matplotlib.pyplot as plt
 import scipy.io
 try:
     import lnp
@@ -23,10 +22,10 @@
     import lnp_checkerflicker as lnpc
 
 main_dir = '/Users/ycan/Documents/official/gottingen/lab rotations/\
-LR3 Gollisch/data/Experiments/Mouse/2016_10_21/'
+LR3 Gollisch/data/Experiments/Mouse/2017_02_14/'
 
 cells_classified = main_dir+'clusters.mat'
-#%%
+
 stimulus_path = '/Users/ycan/Documents/official/gottingen/\
 lab rotations/LR3 Gollisch/data/fff2h.npy'
 frames_path = 'frametimes/3_fff_gauss_2blinks_frametimings.mat'
@@ -44,7 +43,10 @@
 # %%
 first_run_flag = True
 
-for filename in files:
+ooi_dimos = scipy.io.loadmat(main_dir+'/on_bias.mat')['onbias']
+ooi_dimos = ooi_dimos.reshape((ooi_dimos.shape[1],))
+
+for i, filename in enumerate(files):
     if first_run_flag:
         f = scipy.io.loadmat(main_dir+frames_path)
         ftimes = (np.array(f.get('ftimes')/1000))
@@ -100,7 +102,7 @@
     spikecount_stc, peak, onoffindex = lnpc.onoffindex(v[:, 0], bins_stc,
                                                        spikecount_stc)
 
-#%%
+
     np.savez(save_path,
              sta=sta,
              stimulus_type=stimulus_type,
@@ -116,6 +118,6 @@
              spike_path=spike_path,
              total_spikes=total_spikes,
              peak=peak,
-             stimulus_name=stimulus_name
+             stimulus_name=stimulus_name,
+             ooi_dimos=ooi_dimos[i]
              )
-

onoffplotter_dimos.py

@@ -10,108 +10,143 @@
 import matplotlib.pyplot as plt
 
 main_dir = '/Users/ycan/Documents/official/gottingen/lab rotations/\
-LR3 Gollisch/data/Experiments/Mouse/2016_10_21/analyzed/'
-
-
-exp_name = main_dir.split('/')[-4]+'_'+main_dir.split('/')[-3]
-
-allfiles = os.listdir(main_dir)
-
-files_f = []  # Full field flicker
-files_c = []  # Checkerflicker
-
-for i in allfiles:
-    if i[-4:] == '.npz':
-        if i[0] == str(3):
-            files_f.append(i)
-        elif i[0] == str(2):
-            files_c.append(i)
-onoffindices_f = np.array([])
-onoffindices_c = np.array([])
-
-spikenr_f = np.array([])
-spikenr_c = np.array([])
-
-filenames_f = []
-filenames_c = []
-
-exclude_spike_limit = 200
-excluded_f = 0
-excluded_c = 0
-
-for i in files_f:
-    f = np.load(main_dir+i)
-    spikenr_f = np.append(spikenr_f, f['total_spikes'])
-    if spikenr_f[-1] < exclude_spike_limit:
-        spikenr_f = spikenr_f[:-1]
-        excluded_f += 1
-        continue
-    onoffindices_f = np.append(onoffindices_f, f['onoffindex'])
-    filenames_f.append(str(f['filename']))
-
-for i in files_c:
-    f = np.load(main_dir+i)
-    spikenr_c = np.append(spikenr_c, f['total_spikes'])
-    if spikenr_c[-1] < exclude_spike_limit:
-        spikenr_c = spikenr_c[:-1]
-        excluded_c += 1
-        continue
-    onoffindices_c = np.append(onoffindices_c, f['onoffindex'])
-    filenames_c.append(str(f['filename']))
-# %% Only get cells that are in both sets
-filenamesc_f = []
-spikenrc_f = np.array([])
-onoffindicesc_f = np.array([])
-filenamesc_c = []
-spikenrc_c = np.array([])
-onoffindicesc_c = np.array([])
-
-for i in range(len(filenames_f)):
-    if filenames_f[i] in filenames_c:
-        filenamesc_f.append(filenames_f[i])
-        spikenrc_f = np.append(spikenrc_f, spikenr_f[i])
-        onoffindicesc_f = np.append(onoffindicesc_f, onoffindices_f[i])
-for i in range(len(filenames_c)):
-    if filenames_c[i] in filenames_f:
-        filenamesc_c.append(filenames_c[i])
-        spikenrc_c = np.append(spikenrc_c, spikenr_c[i])
-        onoffindicesc_c = np.append(onoffindicesc_c, onoffindices_c[i])
-
-spikenr_f = spikenrc_f
-onoffindices_f = onoffindicesc_f
-spikenr_c = spikenrc_c
-onoffindices_c = onoffindicesc_c
-
-outliers = np.where(np.abs(onoffindices_c - onoffindices_f) > .6)[0]
-
-# %%
-plt.figure(figsize=(8, 16), dpi=200)
-
-plt.subplot(2, 1, 2)
-plt.hist(onoffindices_f, bins=np.linspace(-1, 1, num=40), alpha=.6)
-plt.hist(onoffindices_c, bins=np.linspace(-1, 1, num=40), alpha=.6)
-plt.legend(['Full field', 'Checkerflicker'])
-plt.title('Histogram of On Off indices \n{}'.format(exp_name))
-plt.xlabel('On-off index')
-plt.ylabel('Frequency')
-
-plt.subplot(2, 1, 1)
-plt.scatter(onoffindices_f, onoffindices_c)
-plt.plot(onoffindices_f[outliers], onoffindices_c[outliers], 'r.')
-plt.plot(np.linspace(-1, 1), np.linspace(-1, 1), '--')
-for i in outliers:
-    plt.text(onoffindices_f[i], onoffindices_c[i], filenamesc_c[i])
-plt.title('On-Off indices obtained from Full field vs Checkerflicker\n{}'
-          .format(exp_name))
-plt.ylabel('Checkerflicker')
-plt.xlabel('Full field flicker')
-plt.axis('square')
-
-plt.tight_layout()
-plt.savefig('/Users/ycan/Documents/official/gottingen/lab rotations/\
-LR3 Gollisch/figures/{}'.format(exp_name), dpi=200)
-plt.show()
-
-for i in outliers:
-    print('{:5s} change {:>5.2f} to {:>5.2f}'
-          .format(filenamesc_c[i], onoffindices_f[i], onoffindices_c[i]))
+LR3 Gollisch/data/Experiments/Mouse/'
+
+all_experiments = os.listdir(main_dir)[1:]
+
+for experiment in all_experiments:
+
+    w_dir = '/Users/ycan/Documents/official/gottingen/lab rotations/\
+LR3 Gollisch/data/Experiments/Mouse/'+experiment+'/analyzed/'
+
+    exp_name = w_dir.split('/')[-4]+'_'+w_dir.split('/')[-3]
+
+    allfiles = os.listdir(w_dir)
+
+    files_f = []  # Full field flicker
+    files_c = []  # Checkerflicker
+
+    for i in allfiles:
+        if i[-4:] == '.npz':
+            if i[0] == str(3):
+                files_f.append(i)
+            elif i[0] == str(2):
+                files_c.append(i)
+    onoffindices_f = np.array([])
+    onoffindices_c = np.array([])
+    onoffindices_o = np.array([])
+
+    spikenr_f = np.array([])
+    spikenr_c = np.array([])
+
+    filenames_f = []
+    filenames_c = []
+
+    exclude_spike_limit = 200
+    excluded_f = 0
+    excluded_c = 0
+
+    for index, i in enumerate(files_f):
+        f = np.load(w_dir+i)
+        spikenr_f = np.append(spikenr_f, f['total_spikes'])
+        if spikenr_f[-1] < exclude_spike_limit:
+            spikenr_f = spikenr_f[:-1]
+            excluded_f += 1
+            continue
+        if np.isnan(f['ooi_dimos']):
+            continue
+        onoffindices_f = np.append(onoffindices_f, f['onoffindex'])
+        onoffindices_o = np.append(onoffindices_o, f['ooi_dimos'])
+        filenames_f.append(str(f['filename']))
+
+    for i in files_c:
+        f = np.load(w_dir+i)
+        spikenr_c = np.append(spikenr_c, f['total_spikes'])
+        if spikenr_c[-1] < exclude_spike_limit:
+            spikenr_c = spikenr_c[:-1]
+            excluded_c += 1
+            continue
+        onoffindices_c = np.append(onoffindices_c, f['onoffindex'])
+        filenames_c.append(str(f['filename']))
+    # %% Only get cells that are in both sets
+    filenamesc_f = []
+    spikenrc_f = np.array([])
+    onoffindicesc_f = np.array([])
+    onoffindicesc_o = np.array([])
+    filenamesc_c = []
+    spikenrc_c = np.array([])
+    onoffindicesc_c = np.array([])
+
+    for i in range(len(filenames_f)):
+        if filenames_f[i] in filenames_c:
+            filenamesc_f.append(filenames_f[i])
+            spikenrc_f = np.append(spikenrc_f, spikenr_f[i])
+            onoffindicesc_f = np.append(onoffindicesc_f, onoffindices_f[i])
+            onoffindicesc_o = np.append(onoffindicesc_o, onoffindices_o[i])
+    for i in range(len(filenames_c)):
+        if filenames_c[i] in filenames_f:
+            filenamesc_c.append(filenames_c[i])
+            spikenrc_c = np.append(spikenrc_c, spikenr_c[i])
+            onoffindicesc_c = np.append(onoffindicesc_c, onoffindices_c[i])
+
+    spikenr_f = spikenrc_f
+    onoffindices_f = onoffindicesc_f
+    onoffindices_o = onoffindicesc_o
+    spikenr_c = spikenrc_c
+    onoffindices_c = onoffindicesc_c
+
+    outliers = np.where(np.abs(onoffindices_c - onoffindices_f) > .6)[0]
+
+    r_cf = np.corrcoef(onoffindices_c, onoffindices_f)[1, 0]
+    r_of = np.corrcoef(onoffindices_o, onoffindices_f)[1, 0]
+    r_co = np.corrcoef(onoffindices_c, onoffindices_o)[1, 0]
+
+    axis_limits = [-1.1, 1.1, -1.1, 1.1]
+
+    # %%
+    plt.figure(figsize=(10, 10), dpi=200)
+    plt.suptitle(exp_name)
+
+    plt.subplot(2, 2, 1)
+    plt.hist(onoffindices_f, bins=np.linspace(-1, 1, num=40), alpha=.5)
+    plt.hist(onoffindices_c, bins=np.linspace(-1, 1, num=40), alpha=.5)
+    plt.hist(onoffindices_o, bins=np.linspace(-1, 1, num=40), alpha=.5)
+    plt.legend(['Full field', 'Checkerflicker', 'On off steps'])
+    plt.title('Histogram of On Off indices')
+    plt.xlabel('On-off index')
+    plt.ylabel('Frequency')
+
+    plt.subplot(2, 2, 2)
+    plt.scatter(onoffindices_f, onoffindices_c)
+    plt.plot(onoffindices_f[outliers], onoffindices_c[outliers], 'r.')
+    plt.plot(np.linspace(-1, 1), np.linspace(-1, 1), '--', alpha=.4)
+    plt.text(.7, -1.05, 'R = {:4.2}'.format(r_cf))
+    plt.axis(axis_limits)
+    for i in outliers:
+        plt.text(onoffindices_f[i], onoffindices_c[i], filenamesc_c[i])
+    plt.title('On-Off indices obtained from Full field vs Checkerflicker')
+    plt.ylabel('Checkerflicker')
+    plt.xlabel('Full field flicker')
+
+    plt.subplot(2, 2, 3)
+    plt.scatter(onoffindices_f, onoffindices_o)
+    plt.text(.7, -1.05, 'R = {:4.2}'.format(r_of))
+    plt.plot(np.linspace(-1, 1), np.linspace(-1, 1), '--', alpha = .4)
+    plt.axis(axis_limits)
+    plt.title('fff vs on off steps')
+    plt.xlabel('full field flicker')
+    plt.ylabel('on off steps')
+
+    plt.subplot(2, 2, 4)
+    plt.scatter(onoffindices_c, onoffindices_o)
+    plt.text(.7, -1.05, 'R = {:4.2}'.format(r_co))
+    plt.plot(np.linspace(-1, 1), np.linspace(-1, 1), '--', alpha = .4)
+    plt.axis(axis_limits)
+    plt.title('checkerflicker vs on off steps')
+    plt.xlabel('checkerflicker')
+    plt.ylabel('on off steps')
+
+    plt.tight_layout()
+    plt.subplots_adjust(top=0.90)
+    plt.savefig('/Users/ycan/Documents/official/gottingen/lab rotations/\
+LR3 Gollisch/figures/{}'.format(exp_name), dpi=200)

plotall_dimos.py

@@ -17,9 +17,9 @@
 import matplotlib.pyplot as plt
 
 main_dir = '/Users/ycan/Documents/official/gottingen/lab rotations/\
-LR3 Gollisch/data/Experiments/Mouse/2017_02_14/analyzed/'
+LR3 Gollisch/data/Experiments/Mouse/2017_01_31/analyzed/'
 
-exp_name = main_dir.split('/')[-4]+' '+main_dir.split('/')[-3]
+exp_name = main_dir.split('/')[-4]+'_'+main_dir.split('/')[-3]
 
 allfiles = os.listdir(main_dir)