#what size images are we working with??

width = 256

height = width

frame_ref=400

f_rate=30.

f_low=[.1,.3]

f_high=[1.,3.]

#define the base dirs for the data and analysis

#note that these should become network locations

base_dir_data='/media/cornelis/DataCDH/Raw-data/Test Data'

base_dir_analysis='/media/cornelis/DataCDH/data/Test Data Output'

to_analyze=jf.check_dirs(base_dir_data,base_dir_analysis)

print(to_analyze)

#start a loop on the folders to analyze and do some things.

#we need to make a local copy for speed of loading and saving

base_dir_tmp='/home/cornelis/PycharmProjects/BrainImageAnalyzer/data'

for f in to_analyze:

#Check if the tmp dir exists or not, copy over the dirs in the date folder

if os.path.isdir(base_dir_tmp):

print('tmp found, deleting')

shutil.rmtree(base_dir_tmp)

shutil.copytree(base_dir_data+f,base_dir_tmp)

else:

shutil.copytree(base_dir_data+f,base_dir_tmp)

print('tmp not found, just copying')

#figure out which cages are present

#print('These are the cages '+str(jf.check_cages(base_dir_tmp))+' in'+f)

the_cages=jf.check_cages(base_dir_tmp)

#continue doing stuff

#step one is to read in all the raw data and save all the green videos

if len(the_cages)>0:

for c in the_cages:

#setup the dir for reading the raw data

data_dir=base_dir_tmp+str(c)+'/Videos/'

#which mice are in the cage?

the_mice=jf.check_mice(data_dir)

#print(data_dir)

os.chdir(data_dir)

raw_list=glob.glob('*.raw')

green_dir=base_dir_tmp+c+'/Green/'

os.makedirs(green_dir)

for rf in raw_list:

frames=fj.get_frames(data_dir+rf,width,height)

out_green_fn=rf[:-4]+'.g'

fj.save_to_file(green_dir,out_green_fn,frames,np.uint8)

print('waiting...')

#copy the resulting folder to the analysis location

green_dir_to_copy=base_dir_analysis+f+'/'+c

#print(green_dir_to_copy)

if os.path.isdir(green_dir_to_copy+'/Green/'):

shutil.rmtree(green_dir_to_copy+'/Green/')

shutil.copytree(green_dir,green_dir_to_copy+'/Green/')

else:

shutil.copytree(green_dir,green_dir_to_copy+'/Green/')

#Do alignments!!

print "Doing alignments..."

aligned_dir=base_dir_tmp+c+'/Aligned/'

os.makedirs(aligned_dir)

for m in the_mice:

lof, lofilenames=dj.get_file_list(green_dir, m)

print(lof)

lp=dj.get_distance_var(lof,width,height,frame_ref)

for i in range(len(lp)):

print('Working on this file: ')+str(lof[i])

#tmp_lof=[]

#tmp_lof.append(lof[i])

#print('creating 1 element list')

#print(type(tmp_lof))

frames=dj.get_green_frames(str(lof[i]),width,height)

frames=dj.shift_frames(frames,lp[i])

#save it!

out_aligned_fn=str(lofilenames[i])

out_aligned_fn=out_aligned_fn[:-4]+'_aligned.g'

fj.save_to_file(aligned_dir,out_aligned_fn,frames,np.uint8)

#copy the resulting folder to the analysis location

aligned_dir_to_copy=base_dir_analysis+f+'/'+c

if os.path.isdir(aligned_dir_to_copy+'/Aligned/'):

shutil.rmtree(aligned_dir_to_copy+'/Aligned/')

shutil.copytree(aligned_dir,aligned_dir_to_copy+'/Aligned/')

else:

shutil.copytree(aligned_dir,aligned_dir_to_copy+'/Aligned/')

#Do temporal filters, apply and calculate dff

#each filter band

for i in range(len(f_low)):

#set up a folder for this band

band_dir=base_dir_tmp+c+'/DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/'

#and for GSR version

gsrband_dir=base_dir_tmp+c+'/GSR_DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/'

os.makedirs(band_dir)

os.makedirs(gsrband_dir)

#go to the aligned tmp dir

os.chdir(aligned_dir)

aligned_list=glob.glob('*.g')

for af in aligned_list:

frames=dj.get_green_frames(aligned_dir+af,width,height)

avg_frames=fj.calculate_avg(frames)

frames=fj.cheby_filter(frames, f_low[i], f_high[i], f_rate)

frames+=avg_frames

frames=fj.calculate_df_f0(frames)

#save this

out_dff_fn=af[:-4]+'_DFF_'+str(f_low[i])+'-'+str(f_high[i])+'Hz.raw'

fj.save_to_file(band_dir,out_dff_fn,frames,np.float32)

#do gsr

frames=fj.gsr(frames,width,height)

#save this

out_gsr_fn=af[:-4]+'_GSR_DFF_'+str(f_low[i])+'-'+str(f_high[i])+'Hz.raw'

fj.save_to_file(gsrband_dir,out_gsr_fn,frames,np.float32)

#copy the resulting folder to the analysis location

dff_dir_to_copy=base_dir_analysis+f+'/'+c

if os.path.isdir(dff_dir_to_copy+'/DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/'):

shutil.rmtree(dff_dir_to_copy+'/DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/')

shutil.copytree(band_dir,dff_dir_to_copy+'/DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/')

else:

shutil.copytree(band_dir,dff_dir_to_copy+'/DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/')

gsr_dir_to_copy=base_dir_analysis+f+'/'+c

if os.path.isdir(gsr_dir_to_copy+'/GSR_DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/'):

shutil.rmtree(gsr_dir_to_copy+'/GSR_DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/')

shutil.copytree(gsrband_dir,gsr_dir_to_copy+'/GSR_DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/')

else:

shutil.copytree(gsrband_dir,gsr_dir_to_copy+'/GSR_DFF_Freq_Band_'+str(f_low[i])+'-'+str(f_high[i])+'Hz/')

else:

print('No cages present, sry :(')

#at end of loop make sure to clean up tmp folder