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@@ -4,16 +4,17 @@ Created on Wed Oct 14 11:18:44 2020
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@author: kleisp
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This is a script for getting matrices of snippets around the stimulation pulses in PACK-expressing mice,
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-this can later be used for plotting the snippets on top of each other (in this file below) and for line length calculations (in another file)
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-0.1 Hz and 0.05 Hz need to be treated separately
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-need to load dictionaries containing recIDs with corresponding smrs for using raw data
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+which can later be used for plotting the snippets on top of each other and for line length
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+calculations.
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+Note that recordings with 0.1 Hz and 0.05 Hz illumination need to be treated separately
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+One needs to load dictionaries containing recIDs with corresponding smr filenames for using raw data
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+Abbreviations:
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dict- dictionary
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stim- light pulse
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pre- before light pulse
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post-after light pulse
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snipmat- matrix containing snippets
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-
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"""
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import os
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@@ -29,7 +30,7 @@ os.chdir('C:\EAfiles\EAdetection')
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import core.ea_management as eam
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reload(eam)
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-#%% define functions to extract snippets before and after the stim
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+#%% (1) define functions to extract snippets before and after the stim
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''' 'pre' or 'post' are the snippet length in seconds, here 2 is used, sr=sampling rate (here 500)'''
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# get the spike trace before stimulation (pre):
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@@ -71,7 +72,7 @@ def get_snipmat_post(datatrace, recID, post, stimtimes, sr):
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snipmat[tt] = spiketrace
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return snipmat
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-#%% defining the function to get line length of each snippet(snipmat line length)
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+#%% (2) defining the function to get line length of each snippet(snipmat line length)
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def get_snipmat_linelength(snipmat_pre, snipmat_post, linelength_dict_pre, linelength_dict_post, recID):
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@@ -118,6 +119,7 @@ def get_snipmat_linelength(snipmat_pre, snipmat_post, linelength_dict_pre, linel
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linelength_dict_post[recID]['mean post-pulse linelength/second']=np.mean(linelength_s_list)
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linelength_dict_post[recID]['mean post-pulse linelength']=np.mean(linelength_list)
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linelength_dict_post[recID]['pulse number']=count
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+
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#%% in order to exclude unwanted recordings
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pathtobadrecIDs = 'C:\EAfiles\ID_Dateien\\badrecIDs.txt'
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@@ -127,7 +129,7 @@ with open (pathtobadrecIDs,'r') as f:
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badrecIDs = badrecIDs + badIDs
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-#%% Example of using the script to extract the snipmats
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+#%% (3) Example of using the script to extract the snipmats
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#Saline PACK mice 0.05Hz: get snipmat dicts (for before and after 0.05 Hz pulses) (downsampled data)
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os.chdir('C:\EAfiles\EAdetection')
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@@ -182,7 +184,7 @@ outfile = open(filename, 'wb') #write binary: mit Erlaubnis zu (über)schreiben
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pickle.dump(snipmat_005Hz_post_controls, outfile)
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outfile.close()
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-#%% Example of using the script to create dictionaries with line length before and after 0.05Hz pulses from snipmats above
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+#%% (4) Example of using the script to create dictionaries with line length before and after 0.05Hz pulses from snipmats above
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os.chdir('C:\EAfiles\EAdetection')
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ymlfiles = glob('C:\EAfiles\yml_setup_PK43\*.yml') #takes all yml files from this folder
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