def iterate_over_queries(): channel_name = 'ss_PSD.tif' query_number = 4 df_list = iterate_over_mice(query_number, channel_name) aa.write_dfs_to_excel(df_list, 'blob_synapse', 'psd_q4_ratio.xlsx') channel_name = 'ss_VGluT1.tif' query_number = 5 df_list = iterate_over_mice(query_number, channel_name) aa.write_dfs_to_excel(df_list, 'blob_synapse', 'vglut1_q5_ratio.xlsx') channel_name = 'ss_Synap.tif' query_number = 5 df_list = iterate_over_mice(query_number, channel_name) aa.write_dfs_to_excel(df_list, 'blob_synapse', 'synap_q5_ratio.xlsx') channel_name = 'ss_VGluT2.tif' query_number = 6 df_list = iterate_over_mice(query_number, channel_name) aa.write_dfs_to_excel(df_list, 'blob_synapse', 'vglut2_q6_ratio.xlsx') channel_name = 'ss_Synap.tif' query_number = 6 df_list = iterate_over_mice(query_number, channel_name) aa.write_dfs_to_excel(df_list, 'blob_synapse', 'synap_q6_ratio.xlsx')
def main(): """ Run comparisons """ VGLUT3_df = VGLUT3() sheet_name = '20180424_AT_VGLUT3' fn = '20180424_AT_VGLUT3.xlsx' df_list = [VGLUT3_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ CPU_df = CPU() sheet_name = '20180417_AT_CPU' fn = '20180417_AT_CPU.xlsx' df_list = [CPU_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ COMP_df = COMP() sheet_name = '20180727_Microscope_TBS_NM' fn = '20180727_Microscope_TBS_NM.xlsx' df_list = [COMP_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ NM_Scope_df = NM_Scope() sheet_name = 'NM_Scope' fn = 'NM_Scope.xlsx' df_list = [NM_Scope_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ SAPAP3_df = SAPAP3() sheet_name = '20180320_AT_SAPAP3' fn = '20180320_AT_SAPAP3.xlsx' df_list = [SAPAP3_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): #Do not change """ Run comparisons """ NAME_df = Name() #The "NAME" should match the term used in line 13 sheet_name = 'YYYYMMDD_(project title)' #name of excel sheet fn = 'YYYMMDD_(project title).xlsx' #name of excel file df_list = [NAME_df] # the term inside the brackets must match the _____df in line 155 aa.write_dfs_to_excel(df_list, sheet_name, fn) #Do not change
def main(): """ Run comparisons """ N452_df = N452() sheet_name = '20180202_AT_N452' fn = '20180202_AT_N452.xlsx' df_list = [N452_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run homer comparisons """ homer_df = homer() sheet_name = 'Homer-L113' fn = 'Homer-L113.xlsx' df_list = [homer_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ VMAT2_df = VMAT2() sheet_name = '20180627_N449_VMAT2_Parent' fn = '20180627_N449_VMAT2_Parent.xlsx' df_list = [VMAT2_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ VIP_df = VIP() sheet_name = '20180316_AT_VIP' fn = '20180316_AT_VIP.xlsx' df_list = [VIP_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ GABRA4_df = GABRA4() sheet_name = '20180524_N398A_GABRA4' fn = '20180524_N398A_GABRA4.xlsx' df_list = [GABRA4_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ BASSOON_df = BASSOON() sheet_name = '20180607_L124_Isotype' fn = '20180607_L124_Isotype.xlsx' df_list = [BASSOON_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ N39B_df = N39B() sheet_name = '20180609_N39_N416_N59' fn = '220180609_N39_N416_N59.xlsx' df_list = [N39B_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ SYN3_df = SYN3() sheet_name = '20180124_AT_SYN3_Hip' fn = '20180124_AT_SYN3_Hip.xlsx' df_list = [SYN3_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ cck_df = cask() sheet_name = 'cask-K56A' fn = 'cask-K56A-1,2.xlsx' df_list = [cck_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ ISOTYPE_df = ISOTYPE() sheet_name = '20180620_L106_ISOTYPE' fn = '20180620_L106_ISOTYPE.xlsx' df_list = [ISOTYPE_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ validation_df = validation() sheet_name = 'validation-cortex-6' fn = 'validation-cortex-6.xlsx' df_list = [validation_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ SHANK1_df = SHANK1() sheet_name = '20180216_AT_SHANK1' fn = '20180216_AT_SHANK1.xlsx' df_list = [SHANK1_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run comparisons """ MULTI_df = MULTI() sheet_name = '20180516_N39B_N50_N422_N23B' fn = '20180516_N39B_N50_N422_N23B.xlsx' df_list = [MULTI_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run homer comparisons """ mitochrondia_170906_df = mitochrondia_170906() sheet_name = 'mitochrondia_170906' fn = 'mitochrondia_170906.xlsx' df_list = [mitochrondia_170906_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run homer comparisons """ isotype_specific_df = isotype_specific() sheet_name = 'isotype_specific' fn = 'isotype_specific.xlsx' df_list = [isotype_specific_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """Run pairwise comparisons and save to an excel file""" cav31_dflist = cav31_pairwise() gephyrin_dflist = gephyrin_pairwise() synapsin_dflist = synapsin_pairwise() psd_dflist = psd95_pairwise() vglut1_dflist = vglut1_pairwise() sheet_name = 'Pairwise' fn = 'pairwise_comparisons2.xlsx' df_list = synapsin_dflist + vglut1_dflist + psd_dflist + gephyrin_dflist + cav31_dflist aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run concentration comparisons """ synapsin_df = synapsin_concentrations() glur1_df = glur1_concentrations() glur2_df = glur2_concentrations() glur3_df = glur3_concentrations() nr1_df = nr1_concentrations() sheet_name = 'Concentration' fn = 'concentration_comparisons.xlsx' df_list = [synapsin_df, glur1_df, glur2_df, glur3_df, nr1_df] #df_list = [nr1_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """Run pairwise comparisons and save to an excel file""" gephyrin_df = gephyrin_pairwise() cav31_df = cav31_pairwise() synapsin_df = synapsin_pairwise() psd_df = psd95_pairwise() vglut1_df = vglut1_pairwise() sheet_name = 'Pairwise' fn = 'pairwise_comparisons.xlsx' df_list = [synapsin_df, vglut1_df, psd_df, gephyrin_df, cav31_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): # Output filename fn = 'sact_psd_example.xlsx' sheet_name = 'sact_psd_example' # Determine if file exists. This is only an issue when running on windows if os.path.isfile(fn): print('A sheet with this name already exists; rename sheet and rerun') if socket.gethostname() != 'anish': #this line is optional sys.exit() psd_df = psd_pairwise_comparison() df_list = [psd_df] # Export the dataframe to excel aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): """ Run concentration comparisons """ bassoon_psd_21_df = bassoon_L170921_psd_multipleclones() bassoon_vglut1_21_df = bassoon_L170921_vglut1_multipleclones() bassoon_20 = bassoon_L170920_multipleclones() irsp53_df = irsp53_lowicryl_multipleclones() homer_df = homer_multipleclones() vgat_df = VGAT_LRWhite_multipleclones() collybistin_df = collybistin_multipleclones() gephyrin_df = gephyrin_multipleclones() irsp53_3_df = irsp53_lowicryl_multipleclones3() basson_3_21_df = bassoon_L170921_multipleclones3() sheet_name = 'Multipleclones' fn = 'multipleclones.xlsx' df_list = [gephyrin_df, homer_df, irsp53_df, vgat_df, collybistin_df, bassoon_20, bassoon_vglut1_21_df, bassoon_psd_21_df, basson_3_21_df, irsp53_3_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)
def write_df(vol_name_list, signal_list, output_fn): """Save signal measurement results as a df Paramters --------------- vol_name_list : list of strs signal_list : list of floats output_fn : str - output filename Return ---------------- df : dataframe """ column_labels = ['YFP Size'] df = pd.DataFrame(np.nan, index=vol_name_list, columns=column_labels) df.iloc[:, 0] = signal_list sheet_name = 'YFP Size' df_list = [df] aa.write_dfs_to_excel(df_list, sheet_name, output_fn) return df
def run_list_of_queries(mouse_number, mouse_project_str, sheet_name): """ run queries in a parallel manner Parameters ----------------- mouse_number : int mouse_project_str : str sheet_name : str """ output_foldername = 'results_' + sheet_name query_fn = 'queries/' + mouse_project_str + '_queries.json' data_location = '/Users/anish/Documents/yi_mice/' + \ str(mouse_number) + 'ss_stacks/' hostname = socket.gethostname() if hostname == 'Galicia': data_location = '/data5TB/yi_mice/' + str(mouse_number) + 'ss_stacks' dapi_mask_str_base = '/data5TB/yi_mice/dapi-masks/' + \ str(mouse_number) + 'ss_stacks' print('Query Filename: ', query_fn) print('Data Location: ', data_location) print('OutputFoldername: ', output_foldername) print('Sheetname: ', sheet_name) listOfQueries = syn.loadQueriesJSON(query_fn) resolution = {'res_xy_nm': 100, 'res_z_nm': 70} region_name_base = 'F00' thresh = 0.9 result_list = [] num_workers = mp.cpu_count() - 1 print(num_workers) pool = mp.Pool(num_workers) atet_inputs_list = [] mask_location_str = -1 queryID = 0 foldernames = [] for region_num in range(0, 4): region_name = region_name_base + str(region_num) data_region_location = os.path.join(data_location, region_name) dapi_mask_str = os.path.join(dapi_mask_str_base, region_name) for nQuery, query in enumerate(listOfQueries): foldername = region_name + '-Q' + str(nQuery) foldernames.append(foldername) print(foldername) mask_location_str = -1 #dapi_mask_str = -1 atet_input = { 'query': query, 'queryID': queryID, 'nQuery': nQuery, 'resolution': resolution, 'data_region_location': data_region_location, 'data_location': data_location, 'output_foldername': output_foldername, 'region_name': region_name, 'mask_str': mask_location_str, 'dapi_mask_str': dapi_mask_str, 'mouse_number': mouse_number } atet_inputs_list.append(atet_input) queryID = queryID + 1 # Run processes result_list = pool.map(sa.run_synapse_detection, atet_inputs_list) pool.close() pool.join() print('Get process results from the output queue') sorted_queryresult = sa.organize_result_lists(result_list) mouse_df = sa.create_synapse_df(sorted_queryresult, foldernames) print(mouse_df) fn = sheet_name + '.xlsx' df_list = [mouse_df] aa.write_dfs_to_excel(df_list, sheet_name, fn)