| 1 | """ |
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| 2 | This is the base file reader class most file readers should inherit from. |
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| 3 | All generic functionality required for a file loader/reader is built into this |
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| 4 | class |
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| 5 | """ |
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| 6 | |
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| 7 | import os |
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| 8 | import logging |
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| 9 | import numpy as np |
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| 10 | from abc import abstractmethod |
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| 11 | from loader_exceptions import NoKnownLoaderException, FileContentsException,\ |
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| 12 | DataReaderException, DefaultReaderException |
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| 13 | from data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D,\ |
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| 14 | combine_data_info_with_plottable |
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| 15 | |
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| 16 | logger = logging.getLogger(__name__) |
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| 17 | |
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| 18 | |
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| 19 | class FileReader(object): |
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| 20 | # List of Data1D and Data2D objects to be sent back to data_loader |
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| 21 | output = [] |
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| 22 | # Current plottable_(1D/2D) object being loaded in |
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| 23 | current_dataset = None |
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| 24 | # Current DataInfo object being loaded in |
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| 25 | current_datainfo = None |
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| 26 | # String to describe the type of data this reader can load |
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| 27 | type_name = "ASCII" |
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| 28 | # Wildcards to display |
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| 29 | type = ["Text files (*.txt|*.TXT)"] |
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| 30 | # List of allowed extensions |
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| 31 | ext = ['.txt'] |
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| 32 | # Bypass extension check and try to load anyway |
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| 33 | allow_all = False |
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| 34 | # Able to import the unit converter |
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| 35 | has_converter = True |
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| 36 | # Open file handle |
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| 37 | f_open = None |
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| 38 | # Default value of zero |
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| 39 | _ZERO = 1e-16 |
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| 40 | |
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| 41 | def read(self, filepath): |
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| 42 | """ |
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| 43 | Basic file reader |
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| 44 | |
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| 45 | :param filepath: The full or relative path to a file to be loaded |
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| 46 | """ |
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| 47 | if os.path.isfile(filepath): |
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| 48 | basename, extension = os.path.splitext(os.path.basename(filepath)) |
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| 49 | self.extension = extension.lower() |
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| 50 | # If the file type is not allowed, return nothing |
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| 51 | if self.extension in self.ext or self.allow_all: |
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| 52 | # Try to load the file, but raise an error if unable to. |
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| 53 | try: |
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| 54 | self.f_open = open(filepath, 'rb') |
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| 55 | self.get_file_contents() |
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| 56 | |
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| 57 | except DataReaderException as e: |
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| 58 | self.handle_error_message(e.message) |
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| 59 | except OSError as e: |
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| 60 | # If the file cannot be opened |
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| 61 | msg = "Unable to open file: {}\n".format(filepath) |
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| 62 | msg += e.message |
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| 63 | self.handle_error_message(msg) |
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| 64 | finally: |
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| 65 | # Close the file handle if it is open |
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| 66 | if not self.f_open.closed: |
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| 67 | self.f_open.close() |
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| 68 | if len(self.output) > 0: |
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| 69 | # Sort the data that's been loaded |
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| 70 | self.sort_one_d_data() |
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| 71 | self.sort_two_d_data() |
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| 72 | else: |
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| 73 | msg = "Unable to find file at: {}\n".format(filepath) |
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| 74 | msg += "Please check your file path and try again." |
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| 75 | self.handle_error_message(msg) |
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| 76 | |
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| 77 | # Return a list of parsed entries that data_loader can manage |
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| 78 | return self.output |
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| 79 | |
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| 80 | def handle_error_message(self, msg): |
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| 81 | """ |
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| 82 | Generic error handler to add an error to the current datainfo to |
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| 83 | propogate the error up the error chain. |
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| 84 | :param msg: Error message |
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| 85 | """ |
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| 86 | if isinstance(self.current_datainfo, DataInfo): |
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| 87 | self.current_datainfo.errors.append(msg) |
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| 88 | else: |
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| 89 | logger.warning(msg) |
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| 90 | |
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| 91 | def send_to_output(self): |
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| 92 | """ |
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| 93 | Helper that automatically combines the info and set and then appends it |
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| 94 | to output |
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| 95 | """ |
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| 96 | data_obj = combine_data_info_with_plottable(self.current_dataset, |
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| 97 | self.current_datainfo) |
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| 98 | self.output.append(data_obj) |
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| 99 | |
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| 100 | def sort_one_d_data(self): |
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| 101 | """ |
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| 102 | Sort 1D data along the X axis for consistency |
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| 103 | """ |
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| 104 | final_list = [] |
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| 105 | for data in self.output: |
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| 106 | if isinstance(data, Data1D): |
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| 107 | # Sort data by increasing x and remove 1st point |
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| 108 | ind = np.lexsort((data.y, data.x)) |
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| 109 | data.x = np.asarray([data.x[i] for i in ind]).astype(np.float64) |
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| 110 | data.y = np.asarray([data.y[i] for i in ind]).astype(np.float64) |
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| 111 | if data.dx is not None: |
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| 112 | data.dx = np.asarray([data.dx[i] for i in ind]).astype(np.float64) |
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| 113 | if data.dxl is not None: |
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| 114 | data.dxl = np.asarray([data.dxl[i] for i in ind]).astype(np.float64) |
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| 115 | if data.dxw is not None: |
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| 116 | data.dxw = np.asarray([data.dxw[i] for i in ind]).astype(np.float64) |
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| 117 | if data.dy is not None: |
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| 118 | data.dy = np.asarray([data.dy[i] for i in ind]).astype(np.float64) |
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| 119 | if data.lam is not None: |
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| 120 | data.lam = np.asarray([data.lam[i] for i in ind]).astype(np.float64) |
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| 121 | if data.dlam is not None: |
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| 122 | data.dlam = np.asarray([data.dlam[i] for i in ind]).astype(np.float64) |
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| 123 | if len(data.x > 0): |
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| 124 | data.xmin = np.min(data.x) |
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| 125 | data.xmax = np.max(data.x) |
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| 126 | data.ymin = np.min(data.y) |
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| 127 | data.ymax = np.max(data.y) |
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| 128 | # final_list.append(data) |
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| 129 | # self.output = final_list |
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| 130 | |
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| 131 | def sort_two_d_data(self): |
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| 132 | final_list = [] |
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| 133 | for dataset in self.output: |
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| 134 | if isinstance(dataset, Data2D): |
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| 135 | dataset.data = dataset.data.astype(np.float64) |
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| 136 | dataset.qx_data = dataset.qx_data.astype(np.float64) |
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| 137 | dataset.xmin = np.min(dataset.qx_data) |
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| 138 | dataset.xmax = np.max(dataset.qx_data) |
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| 139 | dataset.qy_data = dataset.qy_data.astype(np.float64) |
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| 140 | dataset.ymin = np.min(dataset.qy_data) |
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| 141 | dataset.ymax = np.max(dataset.qy_data) |
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| 142 | dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data |
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| 143 | + dataset.qy_data * dataset.qy_data) |
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| 144 | if dataset.err_data is not None: |
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| 145 | dataset.err_data = dataset.err_data.astype(np.float64) |
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| 146 | if dataset.dqx_data is not None: |
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| 147 | dataset.dqx_data = dataset.dqx_data.astype(np.float64) |
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| 148 | if dataset.dqy_data is not None: |
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| 149 | dataset.dqy_data = dataset.dqy_data.astype(np.float64) |
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| 150 | if dataset.mask is not None: |
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| 151 | dataset.mask = dataset.mask.astype(dtype=bool) |
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| 152 | |
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| 153 | if len(dataset.data.shape) == 2: |
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| 154 | n_rows, n_cols = dataset.data.shape |
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| 155 | dataset.y_bins = dataset.qy_data[0::int(n_cols)] |
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| 156 | dataset.x_bins = dataset.qx_data[:int(n_cols)] |
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| 157 | dataset.data = dataset.data.flatten() |
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| 158 | # final_list.append(dataset) |
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| 159 | # self.output = final_list |
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| 160 | |
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| 161 | def set_all_to_none(self): |
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| 162 | """ |
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| 163 | Set all mutable values to None for error handling purposes |
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| 164 | """ |
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| 165 | self.current_dataset = None |
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| 166 | self.current_datainfo = None |
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| 167 | self.output = [] |
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| 168 | |
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| 169 | def remove_empty_q_values(self, has_error_dx=False, has_error_dy=False): |
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| 170 | """ |
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| 171 | Remove any point where Q == 0 |
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| 172 | """ |
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| 173 | x = self.current_dataset.x |
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| 174 | self.current_dataset.x = self.current_dataset.x[x != 0] |
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| 175 | self.current_dataset.y = self.current_dataset.y[x != 0] |
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| 176 | self.current_dataset.dy = self.current_dataset.dy[x != 0] if \ |
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| 177 | has_error_dy else np.zeros(len(self.current_dataset.y)) |
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| 178 | self.current_dataset.dx = self.current_dataset.dx[x != 0] if \ |
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| 179 | has_error_dx else np.zeros(len(self.current_dataset.x)) |
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| 180 | |
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| 181 | def reset_data_list(self, no_lines=0): |
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| 182 | """ |
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| 183 | Reset the plottable_1D object |
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| 184 | """ |
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| 185 | # Initialize data sets with arrays the maximum possible size |
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| 186 | x = np.zeros(no_lines) |
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| 187 | y = np.zeros(no_lines) |
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| 188 | dy = np.zeros(no_lines) |
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| 189 | dx = np.zeros(no_lines) |
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| 190 | self.current_dataset = plottable_1D(x, y, dx, dy) |
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| 191 | |
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| 192 | @staticmethod |
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| 193 | def splitline(line): |
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| 194 | """ |
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| 195 | Splits a line into pieces based on common delimeters |
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| 196 | :param line: A single line of text |
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| 197 | :return: list of values |
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| 198 | """ |
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| 199 | # Initial try for CSV (split on ,) |
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| 200 | toks = line.split(',') |
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| 201 | # Now try SCSV (split on ;) |
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| 202 | if len(toks) < 2: |
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| 203 | toks = line.split(';') |
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| 204 | # Now go for whitespace |
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| 205 | if len(toks) < 2: |
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| 206 | toks = line.split() |
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| 207 | return toks |
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| 208 | |
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| 209 | @abstractmethod |
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| 210 | def get_file_contents(self): |
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| 211 | """ |
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| 212 | Reader specific class to access the contents of the file |
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| 213 | All reader classes that inherit from FileReader must implement |
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| 214 | """ |
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| 215 | pass |
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