# Source code for src.g5505_file_reader

    import os

    import numpy as np
    import pandas as pd
    import collections
    from igor2.binarywave import load as loadibw

    import src.g5505_utils as utils
    #import src.metadata_review_lib as metadata
    #from src.metadata_review_lib import parse_attribute

    import yaml
    import h5py

    ROOT_DIR = os.path.abspath(os.curdir)

    def read_xps_ibw_file_as_dict(filename):
        """
        Reads IBW files from the Multiphase Chemistry Group, which contain XPS spectra and acquisition settings,
        and formats the data into a dictionary with the structure {datasets: list of datasets}. Each dataset in the
        list has the following structure:

        {
            'name': 'name',
            'data': data_array,
            'data_units': 'units',
            'shape': data_shape,
            'dtype': data_type
        }

        Parameters
        ----------
        filename : str
            The IBW filename from the Multiphase Chemistry Group beamline.

        Returns
        -------
        file_dict : dict
            A dictionary containing the datasets from the IBW file.

        Raises
        ------
        ValueError
            If the input IBW file is not a valid IBW file.

        """

        file_obj = loadibw(filename)

        required_keys = ['wData','data_units','dimension_units','note']
        if sum([item in required_keys for item in file_obj['wave'].keys()]) < len(required_keys):
            raise ValueError('This is not a valid xps ibw file. It does not satisfy minimum adimissibility criteria.')

        file_dict = {}
        path_tail, path_head = os.path.split(filename)

        # Group name and attributes
        file_dict['name'] = path_head
        file_dict['attributes_dict'] = {}

        # Convert notes of bytes class to string class and split string into a list of elements separated by '\r'.
        notes_list = file_obj['wave']['note'].decode("utf-8").split('\r')
        exclude_list = ['Excitation Energy']
        for item in notes_list:
            if '=' in item:
                key, value = tuple(item.split('='))
                # TODO: check if value can be converted into a numeric type. Now all values are string type
                if not key in exclude_list:
                    file_dict['attributes_dict'][key] = value

        # TODO: talk to Thorsten to see if there is an easier way to access the below attributes
        dimension_labels = file_obj['wave']['dimension_units'].decode("utf-8").split(']')
        file_dict['attributes_dict']['dimension_units'] = [item+']' for item in dimension_labels[0:len(dimension_labels)-1]]

        # Datasets and their attributes

        file_dict['datasets'] = []

        dataset = {}
        dataset['name'] = 'spectrum'
        dataset['data'] = file_obj['wave']['wData']
        dataset['data_units'] = file_obj['wave']['data_units']
        dataset['shape'] = dataset['data'].shape
        dataset['dtype'] = type(dataset['data'])

        # TODO: include energy axis dataset

        file_dict['datasets'].append(dataset)

        return file_dict

    def copy_file_in_group(source_file_path, dest_file_obj : h5py.File, dest_group_name, work_with_copy : bool = True):
        # Create copy of original file to avoid possible file corruption and work with it.

        if work_with_copy:
            tmp_file_path = utils.make_file_copy(source_file_path)
        else:
            tmp_file_path = source_file_path

        # Open backup h5 file and copy complet filesystem directory onto a group in h5file
        with h5py.File(tmp_file_path,'r') as src_file:
            dest_file_obj.copy(source= src_file['/'], dest= dest_group_name)

        if 'tmp_files' in tmp_file_path:
            os.remove(tmp_file_path)

    def read_txt_files_as_dict(filename : str , work_with_copy : bool = True ):

        # Get the directory of the current module
        module_dir = os.path.dirname(__file__)
        # Construct the relative file path
        instrument_configs_path = os.path.join(module_dir, 'instruments', 'text_data_sources.yaml')

        with open(instrument_configs_path,'r') as stream:
            try:
                config_dict = yaml.load(stream, Loader=yaml.FullLoader)
            except yaml.YAMLError as exc:
                print(exc)
        # Verify if file can be read by available intrument configurations.
        if not any(key in filename.replace(os.sep,'/') for key in config_dict.keys()):
            return {}

        #TODO: this may be prone to error if assumed folder structure is non compliant
        file_encoding = config_dict['default']['file_encoding'] #'utf-8'
        separator = config_dict['default']['separator']
        table_header = config_dict['default']['table_header']

        for key in config_dict.keys():
            if key.replace('/',os.sep) in filename:
                file_encoding = config_dict[key].get('file_encoding',file_encoding)
                separator = config_dict[key].get('separator',separator).replace('\\t','\t')
                table_header = config_dict[key].get('table_header',table_header)
                timestamp_variables = config_dict[key].get('timestamp',[])
                datetime_format = config_dict[key].get('datetime_format',[])

                description_dict = {}
                #link_to_description = config_dict[key].get('link_to_description',[]).replace('/',os.sep)
                link_to_description = os.path.join(module_dir,config_dict[key].get('link_to_description',[]).replace('/',os.sep))
                with open(link_to_description,'r') as stream:
                    try:
                        description_dict = yaml.load(stream, Loader=yaml.FullLoader)
                    except yaml.YAMLError as exc:
                        print(exc)
                break
        #if 'None' in table_header:
        #    return {}

        # Read header as a dictionary and detect where data table starts
        header_dict = {}
        data_start = False
        # Work with copy of the file for safety
        if work_with_copy:
            tmp_filename = utils.make_file_copy(source_file_path=filename)
        else:
            tmp_filename = filename

        #with open(tmp_filename,'rb',encoding=file_encoding,errors='ignore') as f:
        with open(tmp_filename,'rb') as f:
            table_preamble = []
            for line_number, line in enumerate(f):

                if table_header in line.decode(file_encoding):
                    list_of_substrings = line.decode(file_encoding).split(separator)

                    # Count occurrences of each substring
                    substring_counts = collections.Counter(list_of_substrings)
                    data_start = True
                    # Generate column names with appended index only for repeated substrings
                    column_names = [f"{i}_{name.strip()}" if substring_counts[name] > 1 else name.strip() for i, name in enumerate(list_of_substrings)]

                    #column_names = [str(i)+'_'+name.strip() for i, name in enumerate(list_of_substrings)]
                    #column_names = []
                    #for i, name in enumerate(list_of_substrings):
                    #    column_names.append(str(i)+'_'+name)

                    #print(line_number, len(column_names ),'\n')
                    break
                # Subdivide line into words, and join them by single space.
                # I asumme this can produce a cleaner line that contains no weird separator characters \t \r or extra spaces and so on.
                list_of_substrings = line.decode(file_encoding).split()
                # TODO: ideally we should use a multilinear string but the yalm parser is not recognizing \n as special character
                #line = ' '.join(list_of_substrings+['\n'])
                #line = ' '.join(list_of_substrings)
                table_preamble.append(' '.join([item for item in list_of_substrings]))# += new_line

        # Represent string values as fixed length strings in the HDF5 file, which need
        # to be decoded as string when we read them. It provides better control than variable strings,
        # at the expense of flexibility.
        # https://docs.h5py.org/en/stable/strings.html

        if table_preamble:
            header_dict["table_preamble"] = utils.convert_string_to_bytes(table_preamble)

        # TODO: it does not work with separator as none :(. fix for RGA
        try:
            df = pd.read_csv(tmp_filename,
                            delimiter = separator,
                            header=line_number,
                            #encoding='latin-1',
                            encoding = file_encoding,
                            names=column_names,
                            skip_blank_lines=True)

            df_numerical_attrs = df.select_dtypes(include ='number')
            df_categorical_attrs = df.select_dtypes(exclude='number')
            numerical_variables = [item for item in df_numerical_attrs.columns]

            # Consolidate into single timestamp column the separate columns 'date' 'time' specified in text_data_source.yaml
            if timestamp_variables:
                #df_categorical_attrs['timestamps'] = [' '.join(df_categorical_attrs.loc[i,timestamp_variables].to_numpy()) for i in df.index]
                #df_categorical_attrs['timestamps'] = [ df_categorical_attrs.loc[i,'0_Date']+' '+df_categorical_attrs.loc[i,'1_Time'] for i in df.index]

                #df_categorical_attrs['timestamps'] = df_categorical_attrs[timestamp_variables].astype(str).agg(' '.join, axis=1)
                timestamps_name = ' '.join(timestamp_variables)
                df_categorical_attrs[ timestamps_name] = df_categorical_attrs[timestamp_variables].astype(str).agg(' '.join, axis=1)

                valid_indices = []
                if datetime_format:
                    df_categorical_attrs[ timestamps_name] = pd.to_datetime(df_categorical_attrs[ timestamps_name],format=datetime_format,errors='coerce')
                    valid_indices = df_categorical_attrs.dropna(subset=[timestamps_name]).index
                    df_categorical_attrs = df_categorical_attrs.loc[valid_indices,:]
                    df_numerical_attrs = df_numerical_attrs.loc[valid_indices,:]

                    df_categorical_attrs[timestamps_name] = df_categorical_attrs[timestamps_name].dt.strftime(config_dict['default']['desired_format'])
                    startdate = df_categorical_attrs[timestamps_name].min()
                    enddate = df_categorical_attrs[timestamps_name].max()

                    df_categorical_attrs[timestamps_name] = df_categorical_attrs[timestamps_name].astype(str)
                    #header_dict.update({'stastrrtdate':startdate,'enddate':enddate})
                    header_dict['startdate']= str(startdate)
                    header_dict['enddate']=str(enddate)

                if len(timestamp_variables) > 1:
                    df_categorical_attrs = df_categorical_attrs.drop(columns = timestamp_variables)

                    #df_categorical_attrs.reindex(drop=True)
                    #df_numerical_attrs.reindex(drop=True)

            categorical_variables = [item for item in df_categorical_attrs.columns]
            ####
            #elif 'RGA' in filename:
            #    df_categorical_attrs = df_categorical_attrs.rename(columns={'0_Time(s)' : 'timestamps'})

            ###
            file_dict = {}
            path_tail, path_head = os.path.split(tmp_filename)

            file_dict['name'] = path_head
            # TODO: review this header dictionary, it may not be the best way to represent header data
            file_dict['attributes_dict'] = header_dict
            file_dict['datasets'] = []
            ####

            df = pd.concat((df_categorical_attrs,df_numerical_attrs),axis=1)

            #if numerical_variables:
            dataset = {}
            dataset['name'] = 'data_table'#_numerical_variables'
            dataset['data'] = utils.dataframe_to_np_structured_array(df) #df_numerical_attrs.to_numpy()
            dataset['shape'] = dataset['data'].shape
            dataset['dtype'] = type(dataset['data'])
            #dataset['data_units'] = file_obj['wave']['data_units']
            #
            # Create attribute descriptions based on description_dict
            dataset['attributes'] = {}

            for column_name in df.columns:
                column_attr_dict = description_dict['table_header'].get(column_name,
                                                                        {'note':'there was no description available. Review instrument files.'})
                dataset['attributes'].update({column_name: utils.parse_attribute(column_attr_dict)})

            #try:
            #    dataset['attributes'] = description_dict['table_header'].copy()
            #    for key in description_dict['table_header'].keys():
            #        if not key in numerical_variables:
            #            dataset['attributes'].pop(key) # delete key
            #        else:
            #            dataset['attributes'][key] = utils.parse_attribute(dataset['attributes'][key])
            #    if timestamps_name in categorical_variables:
            #        dataset['attributes'][timestamps_name] = utils.parse_attribute({'unit':'YYYY-MM-DD HH:MM:SS.ffffff'})
            #except ValueError as err:
            #    print(err)

            file_dict['datasets'].append(dataset)

            #if categorical_variables:
            #    dataset = {}
            #    dataset['name'] = 'table_categorical_variables'
            #    dataset['data'] = dataframe_to_np_structured_array(df_categorical_attrs) #df_categorical_attrs.loc[:,categorical_variables].to_numpy()
            #    dataset['shape'] = dataset['data'].shape
            #    dataset['dtype'] = type(dataset['data'])
            #    if timestamps_name in categorical_variables:
            #        dataset['attributes'] = {timestamps_name: utils.parse_attribute({'unit':'YYYY-MM-DD HH:MM:SS.ffffff'})}
            #    file_dict['datasets'].append(dataset)

        except:
            return {}

        return file_dict

    def main():

        inputfile_dir = '\\\\fs101\\5505\\People\\Juan\\TypicalBeamTime'

        file_dict = read_xps_ibw_file_as_dict(inputfile_dir+'\\SES\\0069069_N1s_495eV.ibw')

        for key in file_dict.keys():
            print(key,file_dict[key])

    if __name__ == '__main__':

        main()

        print(':)')