py-neuromodulation 0.0.3__py3-none-any.whl → 0.0.4__py3-none-any.whl

packages/tmsi/build/lib/TMSiFileFormats/file_formats/poly5_to_edf_converter.py

@@ -1,236 +0,0 @@
-"""
-(c) 2022 Twente Medical Systems International B.V., Oldenzaal The Netherlands
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-    http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-
-#######  #     #   #####   #
-   #     ##   ##  #        
-   #     # # # #  #        #
-   #     #  #  #   #####   #
-   #     #     #        #  #
-   #     #     #        #  #
-   #     #     #  #####    #
-
-/**
- * @file ${poly5_to_edf_converter.py} 
- * @brief Poly5 to EDF converter
- *
- */
-
-
-"""
-
-import sys
-import numpy as np
-import tkinter as tk
-from tkinter import filedialog
-import os
-
-from os.path import join, dirname, realpath
-
-Reader_dir = dirname(realpath(__file__))  # directory of this file
-modules_dir = join(Reader_dir, "../../")  # directory with all modules
-
-from TMSiFileFormats.file_readers import Poly5Reader
-from scipy.signal import sosfiltfilt, butter
-from EDFlib.edfwriter import EDFwriter
-
-
-class Poly5_to_EDF_Converter:
-    def __init__(self, batch=None, filename=None, foldername=None, f_c=0.1):
-        """Converts poly5-file(s) to edf format. Either a single file or all
-        poly5 files in a folder and its subfolders.
-        batch: True or False: convert batch of files or single file
-        filename: full path to file
-        foldername: full path to folder
-        f_c: single value or list of two values; cut-off frequency/frequencies of high pass or bandpass filter"""
-        self.f_c = f_c
-        if not batch:
-            if filename == None:
-                root = tk.Tk()
-                filename = filedialog.askopenfilename()
-                root.withdraw()
-            self.convertFile(filename)
-        else:
-            if foldername == None:
-                root = tk.Tk()
-                foldername = filedialog.askdirectory()
-                root.withdraw()
-            n_poly5 = 0
-            conversion_files = []
-            for root, dirs, files in os.walk(foldername):
-                for file in files:
-                    if file.endswith(".poly5") or file.endswith(".Poly5"):
-                        n_poly5 = n_poly5 + 1
-                        edf_filename = file.replace("poly5", "edf")
-                        edf_filename = edf_filename.replace("Poly5", "edf")
-                        if not os.path.isfile(os.path.join(root, edf_filename)):
-                            conversion_files.append(os.path.join(root, file))
-            print("Convert all poly5-files in folder and subfolders to edf")
-            print("\tFolder: ", foldername)
-            print("\tTotal number of poly5-files: ", n_poly5)
-            print(
-                "\tFiles already converted: ", n_poly5 - len(conversion_files)
-            )
-            print("\tFiles to be converted: ", len(conversion_files))
-            for i in range(len(conversion_files)):
-                print("\n\nConvert file ", i + 1, "of", len(conversion_files))
-                self.convertFile(conversion_files[i])
-
-    def convertFile(self, filename):
-        self._readData(filename)
-        self._remove_empty_samples()
-        self._filter_data()
-        self._write_edf_meta_data()
-        self._write_edf_data()
-
-    def _readData(self, filename):
-        self.data = Poly5Reader(filename)
-        self.fs = self.data.sample_rate
-        self.n_signals = len(self.data.samples)
-
-        self.n_analogue = 0
-        for chan in range(0, self.n_signals):
-            if "Volt" in self.data.ch_unit_names[chan]:
-                # analogue channels
-                self.n_analogue = self.n_analogue + 1
-
-    def _remove_empty_samples(self):
-        """remove padding zeros, based on COUNTER channel"""
-        empty_samples = list(np.where(self.data.samples[-1, :] == 0)[0])
-        self.data.samples = np.delete(self.data.samples, empty_samples, axis=1)
-
-    def _filter_data(self):
-        """low-pass filter data of analogue channels to remove offset and drift"""
-        if not isinstance(self.f_c, list):
-            print(
-                "Data is low-pass filtered with cut-off frequency ",
-                self.f_c,
-                "Hz",
-            )
-            sos = butter(
-                1, self.f_c / (self.fs / 2), btype="highpass", output="sos"
-            )
-            self.data.samples[: self.n_analogue, :] = sosfiltfilt(
-                sos, self.data.samples[: self.n_analogue, :]
-            )
-        else:
-            print(
-                "Data is band-pass filtered with cut-off frequencies ",
-                self.f_c[0],
-                "Hz and",
-                self.f_c[1],
-                "Hz",
-            )
-            sos = butter(
-                1,
-                [self.f_c[0] / (self.fs / 2), self.f_c[1] / (self.fs / 2)],
-                btype="bandpass",
-                output="sos",
-            )
-            self.data.samples[: self.n_analogue, :] = sosfiltfilt(
-                sos, self.data.samples[: self.n_analogue, :]
-            )
-
-    def _write_edf_meta_data(self):
-        """ "write edf meta-data to file"""
-        self.edf_filename = self.data.filename.replace("poly5", "edf")
-        self.edf_filename = self.edf_filename.replace("Poly5", "edf")
-        print("Writing to file ", self.edf_filename)
-
-        self.hdl = EDFwriter(
-            self.edf_filename, EDFwriter.EDFLIB_FILETYPE_EDFPLUS, self.n_signals
-        )
-
-        for chan in range(0, self.n_signals):
-            # write sample frequency, channel name and dimension
-            self.hdl.setSampleFrequency(chan, self.fs)
-            self.hdl.setSignalLabel(chan, self.data.ch_names[chan])
-            self.hdl.setPhysicalDimension(chan, self.data.ch_unit_names[chan])
-
-            # write minima and maxima
-            if max(self.data.samples[chan, :]) == min(
-                self.data.samples[chan, :]
-            ):
-                self.hdl.setPhysicalMaximum(
-                    chan, max(self.data.samples[chan, :]) + 100
-                )
-                self.hdl.setPhysicalMinimum(
-                    chan, min(self.data.samples[chan, :])
-                )
-                self.hdl.setDigitalMaximum(chan, 32767)
-                self.hdl.setDigitalMinimum(chan, -32768)
-            elif "V" in self.data.ch_unit_names[chan]:
-                # analogue channels
-                self.hdl.setPhysicalMaximum(
-                    chan, max(self.data.samples[chan, :])
-                )
-                self.hdl.setPhysicalMinimum(
-                    chan, min(self.data.samples[chan, :])
-                )
-                self.hdl.setDigitalMaximum(chan, 32767)
-                self.hdl.setDigitalMinimum(chan, -32768)
-                if not isinstance(self.f_c, list):
-                    self.hdl.setPreFilter(chan, "HP:" + str(self.f_c) + "Hz")
-                else:
-                    self.hdl.setPreFilter(
-                        chan,
-                        "HP:"
-                        + str(self.f_c[0])
-                        + "Hz LP:"
-                        + str(self.f_c[1])
-                        + "Hz",
-                    )
-            elif "count" in self.data.ch_names[chan].lower():
-                # counter channel
-                self.hdl.setPhysicalMaximum(chan, self.fs)
-                self.hdl.setPhysicalMinimum(chan, 0)
-                self.hdl.setDigitalMaximum(chan, self.fs)
-                self.hdl.setDigitalMinimum(chan, 0)
-            else:
-                # other digital channels
-                self.hdl.setPhysicalMaximum(
-                    chan, max(self.data.samples[chan, :])
-                )
-                if min(self.data.samples[chan, :]) < 0:
-                    self.hdl.setPhysicalMinimum(
-                        chan, min(self.data.samples[chan, :])
-                    )
-                else:
-                    self.hdl.setPhysicalMinimum(chan, 0)
-                self.hdl.setDigitalMaximum(chan, 32767)
-                self.hdl.setDigitalMinimum(chan, -32768)
-
-    def _write_edf_data(self):
-        """write data to edf-file"""
-        n_blocks = np.int64(
-            np.floor((np.size(self.data.samples) / self.n_signals) / self.fs)
-        )
-        fs = self.fs
-
-        for i in range(0, n_blocks):
-            for j in range(0, self.n_signals - 1):
-
-                self.hdl.writeSamples(
-                    self.data.samples[j, i * self.fs : (i + 1) * fs]
-                )
-
-            j = j + 1
-            self.hdl.writeSamples(
-                self.data.samples[j, i * fs : (i + 1) * fs] % fs
-            )
-
-            print("\rProgress: % 0.1f %%" % (100 * i / n_blocks), end="\r")
-
-        self.hdl.close()
-        print("Done writing data")