Finish v0.0.0b2

docs/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = '0.0a8'
+release = '0.0b1'
 
 
 # -- General configuration ---------------------------------------------------
@@ -74,7 +74,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

pysigview/app/main_window.py

@@ -485,9 +485,10 @@ def open_data_source(self, path):
 
                 ann_groups = sm.ODS.get_annotations()
 
-                for ann_group in ann_groups.items():
-                    self.annotations.add_annotation_set(ann_group[1],
-                                                        ann_group[0])
+                if ann_groups is not None:
+                    for ann_group in ann_groups.items():
+                        self.annotations.add_annotation_set(ann_group[1],
+                                                            ann_group[0])
 
         # Fork for buffer usage
         if CONF.get('data_management', 'use_memory_buffer'):

pysigview/core/file_formats/formats.py

@@ -23,7 +23,7 @@
 # Local imports
 from .mefd import mefdHandler
 from .d import dHandler
-
+from .h5 import h5Handler
 
 def extension_evaluator(path):
     """
@@ -39,7 +39,6 @@ def extension_evaluator(path):
     extension = path[path.rindex('.'):]
 
     formats = get_available_file_formats()
-
     file_handler = [x for x in formats if x.extension == extension][0]
 
     if file_handler == []:
@@ -56,6 +55,6 @@ def get_available_file_formats():
     """
 
     # TODO do this automatically in the future
-    supported_file_formats = [mefdHandler(), dHandler()]
+    supported_file_formats = [mefdHandler(), dHandler(), h5Handler()]
 
     return supported_file_formats

pysigview/core/file_formats/h5.py

@@ -0,0 +1,149 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Apr 12 13:49:27 2018
+
+Ing.,Mgr. (MSc.) Jan Cimbálník, PhD.
+Biomedical engineering
+International Clinical Research Center
+St. Anne's University Hospital in Brno
+Czech Republic
+&
+Mayo systems electrophysiology lab
+Mayo Clinic
+200 1st St SW
+Rochester, MN
+United States
+"""
+
+# Std imports
+
+# Third pary imports
+import numpy as np
+import pandas as pd
+
+import h5py
+
+# Local imports
+from ..source_manager import FileDataSource
+
+
+class h5Handler(FileDataSource):
+    def __init__(self):
+        super(h5Handler, self).__init__()
+
+        self.name = 'SignalPlant HDF'
+        self.extension = '.h5'
+
+        self.hf = None
+
+    def load_metadata(self):
+
+        if self.hf is None:
+            self.hf = h5py.File(self._path, 'r')
+
+        try:
+            dataset = self.hf['Data']
+        except:
+            dataset = self.hf['data']
+
+        nsamp = dataset.shape[1]
+
+        if self.hf.attrs.get('time_info'):
+            rec_start = int(self.hf.attrs['time_info'] * 1e6)
+        else:
+            rec_start = 0
+        rec_stop = int(rec_start + (nsamp / self.hf.attrs['Fs']) * 1e6)
+        rec_dur = rec_stop - rec_start
+
+        # Get information about the recording
+        self.recording_info = {}
+        self.recording_info['recording_start'] = rec_start
+        self.recording_info['recording_end'] = rec_stop
+        self.recording_info['recording_duration'] = rec_dur
+        self.recording_info['extension'] = '.h5'
+        self.recording_info['nchan'] = len(self.hf['Info'])
+
+        # Get information about channels
+
+        channel_list = [x for x in self.hf['Info']]
+
+        dmap = np.zeros(len(channel_list),
+                        dtype=[('fsamp', np.float, 1),
+                               ('nsamp', np.int32, 1),
+                               ('ufact', np.float, 1),
+                               ('unit', np.object, 1),
+                               ('channels', np.object, 1),
+                               ('discontinuities', np.ndarray, 1),
+                               ('ch_set', np.bool, 1),
+                               ('uutc_ss', np.int64, 2)])
+
+        for i, channel_info in enumerate(self.hf['Info']):
+            fsamp = self.hf.attrs['Fs']
+            if self.hf.attrs.get('unit'):
+                ufact = 1/self.hf.attrs['unit']
+            else:
+                ufact = 1
+            unit = channel_info[2].decode('UTF-8')
+            start_time = rec_start
+            end_time = rec_stop
+            disconts = np.c_[rec_start, rec_start]
+
+            dmap[i] = (fsamp, nsamp, ufact, unit,
+                       channel_info[0].decode('UTF-8'), disconts,
+                       True, [start_time, end_time])
+
+        self.data_map.setup_data_map(dmap)
+
+    def get_annotations(self):
+        """
+        Returns:
+        --------
+        Annotations - in form of pandas DataFrame(s)
+        """
+
+        return None
+
+    def get_data(self, data_map):
+        """
+        Parameters:
+        -----------
+        data_map - DataMap instance for loading
+
+        Returns:
+        --------
+        The data in a list specified by channel_map
+        """
+
+        channel_map = data_map.get_active_channels()
+        uutc_ss = data_map.get_active_largest_ss()
+
+        if self.hf is None:
+            self.hf = h5py.File(self._path, 'r')
+
+        channels = [x[0].decode('UTF-8') for x in self.hf['Info']]
+
+        if self.hf.attrs.get('time_info') is not None:
+            rec_start = int(self.hf.attrs['time_info'] * 1e6)
+        else:
+            rec_start = 0
+        samp_ss = [int(((x-rec_start)/1e6)*self.hf.attrs['Fs'])
+                   for x in uutc_ss]
+
+        channel_idxs = [i for i, x in enumerate(channels)
+                        if x in channel_map]
+
+        try:
+            dataset = self.hf['Data']
+        except:
+            dataset = self.hf['data']
+        dmat = dataset.value[channel_idxs, samp_ss[0]: samp_ss[1]]
+
+        data_out = np.empty(len(data_map), object)
+        for i in range(len(data_map)):
+            data_out[i] = np.array([], dtype='float32')
+        for i, ch in enumerate(channel_map):
+            ch_pos = np.argwhere(data_map['channels'] == ch)[0][0]
+            data_out[ch_pos] = dmat[i]
+
+        return data_out

pysigview/core/file_formats/mefd.py

@@ -69,13 +69,13 @@ def load_metadata(self):
         self.recording_info['nchan'] = len(channel_list)
 
         dmap = np.zeros(len(channel_list),
-                        dtype=[('fsamp', np.float, 1),
-                               ('nsamp', np.int32, 1),
-                               ('ufact', np.float, 1),
-                               ('unit', np.object, 1),
-                               ('channels', np.object, 1),
-                               ('discontinuities', np.ndarray, 1),
-                               ('ch_set', np.bool, 1),
+                        dtype=[('fsamp', np.float),
+                               ('nsamp', np.int32),
+                               ('ufact', np.float),
+                               ('unit', np.object),
+                               ('channels', np.object),
+                               ('discontinuities', np.ndarray),
+                               ('ch_set', np.bool),
                                ('uutc_ss', np.int64, 2)])
 
         for i, channel in enumerate(channel_list):

pysigview/core/source_manager.py

@@ -35,8 +35,8 @@ class DataMap:
     def __init__(self):
         super(DataMap, self).__init__()
 
-        self._map = np.array([], dtype=[('channels', object, 1),
-                                        ('ch_set', np.bool, 1),
+        self._map = np.array([], dtype=[('channels', object),
+                                        ('ch_set', np.bool),
                                         ('uutc_ss', np.int64, 2)])
 
     def __getitem__(self, item):

pysigview/plugins/measurement.py

@@ -61,7 +61,6 @@ def __init__(self, parent):
 
         # Setup camera
         self.signal_camera = SignalCamera()
-        self.spectrogram_camera = SignalCamera()
         self.spectrum_camera = SignalCamera()
 
         self.canvas = scene.SceneCanvas(show=True, keys='interactive',
@@ -147,13 +146,14 @@ def set_spect_type(self, stype):
         if stype == 'spectrum':
             self.spectrum_line.visible = True
             self.spectrogram.visible = False
-            self.spectrum_xaxis.axis._axis_label.text = 'Frequency [Hz]'
-            self.spectrum_view.camera = self.spectrum_camera
+            self.spectrum_xaxis.axis.axis_label = 'Frequency [Hz]'
+            self.spectrum_yaxis.axis.axis_label = 'Amplitude'
+
         elif stype == 'spectrogram':
             self.spectrogram.visible = True
             self.spectrum_line.visible = False
-            self.spectrum_xaxis.axis._axis_label.text = 'Time [s]'
-            self.spectrum_view.camera = self.spectrogram_camera
+            self.spectrum_xaxis.axis.axis_label = 'Time [s]'
+            self.spectrum_yaxis.axis.axis_label = 'Frequency [Hz]'
 
         self.update_signals()
 
@@ -315,17 +315,14 @@ def update_signals(self):
             scale = [s_x, s_y, s_z]
             self.spectrogram.transform = STTransform(scale)
 
-            # Adjust camera limits
-            pos = (0, 0)
-            size = (len(data) * 10 / self.curr_pc.fsamp, freqs[-1])
-            self.spectrogram_camera.limit_rect = pos, size
-
             # Adjust camera view
             freqs = freqs[low_lim_idx:high_lim_idx-1]
             pos = (0, freqs[0])
             size = (len(data) / self.curr_pc.fsamp, freqs[-1] - freqs[0])
-            self.spectrogram_camera.rect = pos, size
+            self.spectrum_camera.rect = pos, size
 
+            # Adjust camera limits
+            self.spectrum_camera.limit_rect = pos, size
 
 class GeneralTools(QWidget):
 
@@ -526,11 +523,11 @@ def set_clim_low_s(self, val):
         # Adjust text
         self.clim_low_le.setText(str(low))
 
-        if self.spectrogram.data is None:
+        if self.spectrogram._data is None:
             return
 
-        d_min = np.min(self.spectrogram.data)
-        d_max = np.max(self.spectrogram.data)
+        d_min = np.min(self.spectrogram._data)
+        d_max = np.max(self.spectrogram._data)
         d_diff = d_max - d_min
         low = ((low/100) * d_diff) + d_min
         high = ((high/100) * d_diff) + d_min
@@ -546,11 +543,11 @@ def set_clim_high_s(self, val):
         # Adjust text
         self.clim_high_le.setText(str(high))
 
-        if self.spectrogram.data is None:
+        if self.spectrogram._data is None:
             return
 
-        d_min = np.min(self.spectrogram.data)
-        d_max = np.max(self.spectrogram.data)
+        d_min = np.min(self.spectrogram._data)
+        d_max = np.max(self.spectrogram._data)
         d_diff = d_max - d_min
         low = ((low/100) * d_diff) + d_min
         high = ((high/100) * d_diff) + d_min