''' Creates .lst file for single wavelength TIFF files (pre-calculated RATIO) in the format used in Trondheim Author: Giovanni, Dec 2021, based on template in VIEW folder by Ajay Expected data structure: In the folder "01_DATA", each animal has a folder, e.g. "190815_h2_El", and located in that folder are all .tif files for that animal There is a sister folder "02_LISTS" Output: In the folder "02_LISTS": There will be a file Animal.lst.xlsx, e.g. "190815_h2_El.lst.xlsx" That file contains one line for each measurement. What to do next? In this file, change values that are global or insert a function that can extract odor name or concentration name from somewhere In the Animal.lst.xlsx file, correct/complete entries (e.g. odor names, odor concentrations) Make sure stimulus timing information is correct Why do I need a .lst.xlsx file? Load measurements in pyVIEW using this .lst file, so that stimulus information is correct For off-line analysis, information is taken from this file. Good to know: Information, where possible, is taken from the OME header of the incoming tif file. If that information is wrong, incomplete, or else, modify the code in: importers.py:P1DualWavelengthTIFSingleFileImporter:parse_metadata ''' from view.python_core.measurement_list import MeasurementList from view.python_core.measurement_list.importers import get_importer_class from view.python_core.flags import FlagsManager from collections import OrderedDict import pandas as pd import logging import pathlib as pl logging.basicConfig(level=logging.INFO) # ------------------- Some parameters about experimental setup, data structure and output file type -------------------- # 3 for single wavelength Till Photonics Measurements # 4 for two wavelength Till Photonics Measurements # 20 for Zeiss Confocal Measurements LE_loadExp = 33 #for Bente, 33 or 35 both work! # Mother of all Folders of your dataset # On Windows, if you copy paths from the file explorer, make sure the string below is always of the form r"......" STG_MotherOfAllFolders = r"/Users/galizia/Nextcloud/VTK_2021/Bente_Test_2021" # path of the "Data" folder in VIEW organization containing the data # On Windows, if you copy paths from the file explorer, make sure the string below is always of the form r"......" STG_Datapath = r"" # path of the "Lists" folder in VIEW organization containing the list files # On Windows, if you copy paths from the file explorer, make sure the string below is always of the form r"......" STG_OdorInfoPath = r"" # Choose measurement list output extension among ".lst", ".lst.xlsx", ".settings.xlsx" # VIEW does not support writing .xls list files anymore (nonetheless, it can read them and revise/update them to .xlsx) measurement_output_extension = ".lst.xlsx" # ------------------- A dictionary containing default values for metadata.---------------------------------------------- # ------------------- Only metadata included in this dictionary will be written ---------------------------------------- # ----Note that columns of the output measeurement list files will have the same order as below.------------------------ default_values = OrderedDict() default_values['Measu'] = 0 # unique identifier for each line, corresponds to item in TILL photonics log file default_values['Label'] = "none" default_values['Odour'] = 'odor?' # stimulus name, maybe extracted from label in the function "custom_func" below default_values['OConc'] = 0 # odor concentration, maybe extracted from label in the function "custom_func" below default_values['Analyze'] = -1 # whether to analyze in VIEWoff. Default 1 default_values['Cycle'] = 0 # how many ms per frame default_values['DBB1'] = 'none' # file name of raw data default_values['UTC'] = 0 # recording time, extracted from file default_values['PxSzX'] = '0.0' # um per pixel, 1.5625 for 50x air objective, measured by Hanna Schnell July 2017 on Till vision system, with a binning of 8 default_values['PxSzY'] = '0.0' # um per pixel, 1.5625 for 50x air objective, measured by Hanna Schnell July 2017 on Till vision system, with a binning of 8 default_values['Lambda'] = 0 # wavelength of stimulus. In TILL, from .log file, In Zeiss LSM, from .lsm file # These will be automatically filed for LE_loadExp=4 default_values['dbb2'] = 'none' # file name of raw data in dual wavelength recordings (FURA) # To include more columns, uncomment entries below and specify a default value. # # # block for first stimulus # default_values['StimON'] = -1 # stimulus onset, unit: frames, count starts at frame 1. # default_values['StimOFF'] = -1 # stimulus offset, unit: frames, count starts at frame 1. # default_values['StimLen'] = 0 # stimulus onset in ms from beginning - alternative to StimON # default_values['StimONms'] = -1 # stimulus length in ms - alternative to StimOFF # # # block for second stimulus # default_values['Stim2ON'] = 0 # stimulus onset, unit: frames, count starts at frame 1. # default_values['Stim2OFF'] = 0 # stimulus offset, unit: frames, count starts at frame 1. # default_values['Stim2Len'] = 0 # stimulus onset in ms from beginning - alternative to StimON # default_values['Stim2ONms'] = -1 # stimulus length in ms - alternative to StimOFF # # # default_values['Age'] = -1 # default_values['Sex'] = 'o' # default_values['Side'] = 'none' # default_values['Comment'] = 'none' # # # default_values['MTime'] = 0 # default_values['Control'] = 0 # default_values['Pharma'] = 'none' # default_values['PhTime'] = 0 # default_values['PhConc'] = 0 # default_values['ShiftX'] = 0 # default_values['ShiftY'] = 0 # default_values['StimISI'] = 0 # default_values['setting'] = 'none' # default_values['dbb3'] = 'none' # default_values['PosZ'] = 0 # default_values['Countl'] = 0 # default_values['slvFlip'] = 0 # ---------------------------------------------------------------------------------------------------------------------- # ----------------- A function used to modify list entries after automatic parsing of metadata ------------------------- # ----------------- This function indicates what needs to be done for a row -------------------------------------------- # ----------------- The same is internally applied to all rows of the measurement list---------------------------------- def get_odorinfo_from_label(label): # format for file name (label) is: # odor_concentration_anything_else.tif # separating element is underscore # is the information for a concentration present? Detect "-" parts = label.split("_") if len(parts) > 1: odor = parts[0] concentration = parts[1] # in the case the name is odor_conc.tif: if concentration[-4:] == '.tif': concentration = concentration[:-4] else: odor = 'odor?' concentration = 'conc?' return [odor, concentration] def custom_func(list_row: pd.Series, animal_tag: str) -> pd.Series: # Examples: # list_row["StimON"] = 25 # list_row["Odour"] = get_odor_from_label(list_row["Label"]) # if list_row["Measu"] # get Odor from another file based on the value of and list_row["Label"] list_row["StimONms"] = '3000' list_row["StimLen"] = '2000' list_row["Comment"] = 'create_measurement_list_ratio' list_row["Line"] = 'ham' #extract odor and concentration from name (list_row["Odour"],list_row["OConc"]) = get_odorinfo_from_label(list_row["Label"]) try: float(list_row["OConc"]) except: #Odour concentration is not a number, set to fictive 0 list_row["OConc"] = '0.0' if list_row["Label"][-4:] == '.tif': list_row["Label"] = list_row["Label"][:-4] return list_row # ---------------------------------------------------------------------------------------------------------------------- # ------------------ A function defining the criteria for excluding measurements --------------------------------------- # ------------------ Currently applicable only for tillvision setups --------------------------------------------------- def measurement_filter(s): # exclude blocks that have in the name "Snapshot" or "Delta" # or that do not have any "_" name = s["Label"] label_not_okay = name.count('Snapshot') > 0 or name.count('Delta') > 0 or name.count('_') < 1 label_okay = not label_not_okay # exclude blocks with less than two frames or no calibration atleast_two_frames = False if type(s["Timing_ms"]) is str: if len(s["Timing_ms"].split(' ')) >= 2 and s["Timing_ms"] != "(No calibration available)": atleast_two_frames = True return label_okay and atleast_two_frames # ______________________________________________________________________________________________________________________ # ------------------ names of columns that will be overwritten by old values ------------------------------------------- # ------ these will only be used if a measurement list file with the same name as current output file exists ----------- overwrite_old_values = ["Line", "PxSzX", "PxSzY", "Age", "Sex", "Prefer", "Comment", "Analyze", "Odour", "OConc"] # ______________________________________________________________________________________________________________________ if __name__ == "__main__": # initialize a FlagsManager object with values specified above flags = FlagsManager() flags.update_flags({"STG_MotherOfAllFolders": STG_MotherOfAllFolders, "STG_OdorInfoPath": STG_OdorInfoPath, "STG_Datapath": STG_Datapath}) # initialize importer importer_class = get_importer_class(LE_loadExp) importer = importer_class(default_values) # open a dialog for choosing raw data files # this returns a dictionary where keys are animal tags (STG_ReportTag) and # values are lists of associated raw data files animal_tag_raw_data_mapping = importer.ask_for_files(default_dir=flags["STG_Datapath"]) # make sure some files were chosen assert len(animal_tag_raw_data_mapping) > 0, IOError("No files were chosen!") for animal_tag, raw_data_files in animal_tag_raw_data_mapping.items(): # automatically parse metadata metadata_df = importer.import_metadata(raw_data_files=raw_data_files, measurement_filter=measurement_filter) # inform user if no usable measurements were found if metadata_df.shape[0] == 0: logging.info(f"No usable measurements we found among the files " f"chosen for the animal {animal_tag}. Not creating a list file") else: # create a new Measurement list object from parsed metadata measurement_list = MeasurementList.create_from_df(LE_loadExp=LE_loadExp, df=metadata_df) # apply custom modifications measurement_list.update_from_custom_func(custom_func=custom_func, animal_tag=animal_tag) # set anaylze to 0 if raw data files don't exist flags.update_flags({"STG_ReportTag": animal_tag}) measurement_list.sanitize(flags=flags, data_file_extensions=importer.movie_data_extensions) # sort by time as in column "UTC" #sorted_df = df.sort_values(by=['Column_name'], ascending=True) # does not work if the list file already existed. measurement_list.measurement_list_df = measurement_list.measurement_list_df.sort_values(by=['UTC'], ascending=True) # construct the name of the output file #AskAjay - what I am writing seems crude to me (Giovanni Dec 21) #Ajay: out_file = f"{flags.get_lst_file_stem()}{measurement_output_extension}" singlefilein = pl.Path(raw_data_files[0]) #singlefilein could be: #'/Users/galizia/Nextcloud/VTK_2021/Bente_Test_2021/01_DATA/190815_h2_El/B_1.tif' #output should be: #'/Users/galizia/Nextcloud/VTK_2021/Bente_Test_2021/02_ANALYSIS/190815_h2_El.lst.xlsx' out_file = pl.Path(singlefilein.parent.parent.parent) out_file = pl.Path.joinpath(out_file, '02_LISTS' , singlefilein.parts[-2]) out_file = f"{out_file}{measurement_output_extension}" # write measurement file to list measurement_list.write_to_list_file(lst_fle=out_file, columns2write=default_values.keys(), overwrite_old_values=overwrite_old_values)