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pyBOAT
Commit e0849c2c authored by Gregor Moenke's avatar Gregor Moenke
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fixed export Windows file paths

parent b7ddb7fa
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Showing with 90 additions and 44 deletions
CHANGELOG.md
View file @ e0849c2c
### pyBOAT 0.8.21
- Fixed export paths for Windows platforms
- Fixed synthetic signal generator AR(1) alpha setting
- Added batch export of wavelet spectra w/o ridges
### pyBOAT 0.8.20
- Added time averaging of Wavelet spectra <-> Fourier estimates
......
pyboat/__init__.py
View file @ e0849c2c
......@@ -3,7 +3,7 @@
import sys,os
import argparse
__version__ = '0.8.20'
__version__ = '0.8.21'
# the object oriented API
from .api import WAnalyzer
......
pyboat/ui/analysis.py
View file @ e0849c2c
......@@ -625,11 +625,12 @@ class WaveletReadoutWindow(QWidget):
options = QFileDialog.Options()
# ----------------------------------------------------------
default_name = os.getenv("HOME") + "/TFAres_" + str(self.signal_id)
format_filter = "Text File (*.txt);; CSV ( *.csv);; Excel (*.xlsx)"
base_name = str(self.signal_id).replace(' ', '-')
default_name = os.path.join(os.getenv("HOME"), base_name + '_ridgeRO')
format_filter = "Text File (*.txt);; csv ( *.csv);; MS Excel (*.xlsx)"
# -----------------------------------------------------------
file_name, sel_filter = dialog.getSaveFileName(
self, "Save as", default_name, format_filter, "(*.txt)", options=options
self, "Save ridge readout as", default_name, format_filter, "(*.txt)", options=options
)
# dialog cancelled
......
pyboat/ui/batch_process.py
View file @ e0849c2c
......@@ -18,6 +18,10 @@ import pyboat
from pyboat import plotting as pl
from pyboat import ensemble_measures as em
# --- resolution of the output plots ---
DPI = 250
class BatchProcessWindow(QMainWindow):
'''
......@@ -58,8 +62,8 @@ class BatchProcessWindow(QMainWindow):
# -- Ridge Analysis Options --
ridge_options = QGroupBox('Ridge Extraction Options')
ridge_options = QGroupBox('Ridge Detection')
thresh_label = QLabel("Ridge Threshold:")
thresh_edit = QLineEdit()
thresh_edit.setValidator(posfloatV)
......@@ -87,13 +91,13 @@ class BatchProcessWindow(QMainWindow):
# -- Plotting Options --
plotting_options = QGroupBox('Ensemble Summary Statistics')
plotting_options = QGroupBox('Summary Statistics')
self.cb_power_dis = QCheckBox('Ridge Power Distribution')
self.cb_power_dis.setStatusTip('Show time-averaged ridge powers distribution')
self.cb_power_dis.setStatusTip('Show time-averaged distribution of ridge powers')
self.cb_plot_ens_dynamics = QCheckBox('Ensemble Dynamics')
self.cb_plot_ens_dynamics.setStatusTip('Show period, amplitude and phase distribution over time')
self.cb_plot_Fourier_dis = QCheckBox('Fourier Spectra Distribution')
self.cb_plot_Fourier_dis.setStatusTip('Distribution of the time averaged Wavelet spectra')
self.cb_plot_Fourier_dis.setStatusTip('Power distribution of the time averaged Wavelet spectra')
lo = QGridLayout()
lo.addWidget(self.cb_plot_ens_dynamics,0,0)
......@@ -110,6 +114,9 @@ class BatchProcessWindow(QMainWindow):
self.cb_specs = QCheckBox('Wavelet Spectra')
self.cb_specs.setStatusTip("Saves the individual wavelet spectra as images (png's)")
self.cb_specs_noridge = QCheckBox('Wavelet Spectra w/o ridges')
self.cb_specs_noridge.setStatusTip("Saves the individual wavelet spectra without the ridges as images (png's)")
self.cb_readout = QCheckBox('Ridge Readouts')
self.cb_readout.setStatusTip('Saves one data frame per signal to disc as csv')
......@@ -123,11 +130,9 @@ class BatchProcessWindow(QMainWindow):
self.cb_save_Fourier_dis = QCheckBox('Fourier Distribution')
self.cb_save_Fourier_dis.setStatusTip("Saves median and quartiles of the Fourier power spectral distribution")
home = expanduser("~")
OutPath_label = QLabel('Export to:')
self.OutPath_edit = QLineEdit(home)
if self.debug:
self.OutPath_edit.setText(home + '/Desktop/wres')
# defaults to HOME
self.OutPath_edit = QLineEdit( expanduser('~') )
PathButton = QPushButton('Select Path..')
PathButton.setMaximumWidth(100)
......@@ -144,8 +149,10 @@ class BatchProcessWindow(QMainWindow):
lo = QGridLayout()
lo.setSpacing(1.5)
lo.addWidget(self.cb_specs,0,0)
lo.addWidget(self.cb_readout,1,0)
lo.addWidget(self.cb_readout_plots,2,0)
lo.addWidget(self.cb_specs_noridge,1,0)
lo.addWidget(self.cb_readout,2,0)
lo.addWidget(self.cb_readout_plots,3,0)
#lo.addWidget(line1, 3,0)
lo.addWidget(self.cb_sorted_powers,4,0)
lo.addWidget(self.cb_save_ensemble_dynamics,5,0)
......@@ -185,8 +192,9 @@ class BatchProcessWindow(QMainWindow):
# -- main layout --
main_layout.addWidget(ridge_options, 0, 0, 1, 1)
main_layout.addWidget(plotting_options, 1, 0, 1, 1)
main_layout.addWidget(plotting_options, 0, 0, 1, 1)
main_layout.addWidget(ridge_options, 1, 0, 1, 1)
main_layout.addWidget(export_options, 0, 1, 2, 1)
main_layout.addWidget(process_box, 2, 0, 1, 2)
......@@ -238,7 +246,7 @@ class BatchProcessWindow(QMainWindow):
# save out the sorted average powers
if self.export_options.isChecked() and self.cb_sorted_powers.isChecked():
fname = f'{OutPath}/average-ridge-powers_{dataset_name}.csv'
fname = os.path.join(OutPath, f'{dataset_name}_ridge-powers.csv')
powers_series.to_csv(fname, sep = ',', index = True, header = False)
# --- compute summary statistics over time ---
......@@ -261,7 +269,7 @@ class BatchProcessWindow(QMainWindow):
for obs, df in zip(
['periods', 'amplitudes', 'powers', 'phasesR'], res
):
fname = f'{OutPath}/{obs}_{dataset_name}.csv'
fname = os.path.join(OutPath, f'{dataset_name}_{obs}.csv')
df.index = tvec
df.index.name = 'time'
df.to_csv(fname, sep = ',', float_format = '%.3f')
......@@ -277,7 +285,7 @@ class BatchProcessWindow(QMainWindow):
if self.export_options.isChecked() and self.cb_save_Fourier_dis.isChecked():
fname = f'{OutPath}/fourier-distribution_{dataset_name}.csv'
fname = os.path.join(OutPath, f'{dataset_name}_fourier-distribution.csv')
# save out median and quartiles of Fourier powers
df_fdis = pd.DataFrame(index = df_fouriers.index)
......@@ -364,7 +372,7 @@ class BatchProcessWindow(QMainWindow):
dialog.setOption(QFileDialog.ShowDirsOnly, False)
dir_name = dialog.getExistingDirectory(
self, "Select a folder to save the results", os.getenv("HOME")
self, "Select a folder to save the results", expanduser('~'),
)
# dialog cancelled
......@@ -474,6 +482,7 @@ class BatchProcessWindow(QMainWindow):
# -- Save out individual results --
if self.cb_specs.isChecked():
# plot spectrum and ridge
ax_sig, ax_spec = pl.mk_signal_modulus_ax(self.parentDV.time_unit)
pl.plot_signal_modulus((ax_sig, ax_spec),
......@@ -483,24 +492,40 @@ class BatchProcessWindow(QMainWindow):
p_max = self.wlet_pars['p_max'])
pl.draw_Wavelet_ridge(ax_spec, ridge_data)
plt.tight_layout()
fname = f'{OutPath}/{signal_id}_wspec.png'
fname = os.path.join(OutPath, f'{signal_id}_wspec.png')
if self.debug:
print(f'Plotting and saving {signal_id} to {fname}')
plt.savefig(fname)
print(f'Plotting and saving spectrum {signal_id} to {fname}')
plt.savefig(fname, dpi = DPI)
plt.close()
if self.cb_specs_noridge.isChecked():
# plot spectrum without ridge
ax_sig, ax_spec = pl.mk_signal_modulus_ax(self.parentDV.time_unit)
pl.plot_signal_modulus((ax_sig, ax_spec),
tvec, signal,
modulus,
periods,
p_max = self.wlet_pars['p_max'])
plt.tight_layout()
fname = os.path.join(OutPath, f'{signal_id}_wspecNR.png')
if self.debug:
print(f'Plotting and saving spectrum {signal_id} to {fname}')
plt.savefig(fname, dpi = DPI)
plt.close()
if self.cb_readout_plots.isChecked() and not ridge_data.empty:
pl.plot_readout(ridge_data)
fname = f'{OutPath}/{signal_id}_readout.png'
fname = os.path.join(OutPath, f'{signal_id}_readout.png')
if self.debug:
print(f'Plotting and saving {signal_id} to {fname}')
plt.savefig(fname)
plt.savefig(fname, dpi = DPI)
plt.close()
if self.cb_readout.isChecked() and not ridge_data.empty:
fname = f'{OutPath}/{signal_id}_readout.csv'
fname = os.path.join(OutPath, f'{signal_id}_readout.csv')
if self.debug:
print(f'Saving ridge reatout to {fname}')
ridge_data.to_csv(fname, sep = ',', float_format = '%.3f', index = False)
......@@ -606,7 +631,7 @@ class FourierDistributionWindow(QWidget):
time_unit = self.time_unit,
fig = Canvas.fig)
Canvas.fig.subplots_adjust(wspace = 0.3, left = 0.1, top = 0.98,
Canvas.fig.subplots_adjust(wspace = 0.3, left = 0.15, top = 0.98,
right = 0.95, bottom = 0.15)
main_layout = QGridLayout()
main_layout.addWidget(Canvas,0,0,9,1)
......
pyboat/ui/data_viewer.py
View file @ e0849c2c
import sys, os
from os.path import expanduser
import numpy as np
from PyQt5.QtWidgets import (
......@@ -1034,8 +1035,9 @@ class DataViewer(QMainWindow):
options = QFileDialog.Options()
# ----------------------------------------------------------
default_name = "trend_" + str(self.signal_id)
format_filter = "Text File (*.txt);; CSV ( *.csv);; Excel (*.xlsx)"
base_name = str(self.signal_id).replace(' ', '-')
default_name = os.path.join(expanduser('~'), base_name + '_trend')
format_filter = "Text File (*.txt);; csv ( *.csv);; MS Excel (*.xlsx)"
# -----------------------------------------------------------
file_name, sel_filter = dialog.getSaveFileName(
self, "Save as", default_name, format_filter, None, options=options
......@@ -1063,7 +1065,7 @@ class DataViewer(QMainWindow):
# ------the write out calls to pandas----------------
float_format = "%.2f" # still old style :/
float_format = "%.3f" # still old style :/
if file_ext == "txt":
df_out.to_csv(file_name, index=False, sep="\t", float_format=float_format)
......
pyboat/ui/synth_gen.py
View file @ e0849c2c
......@@ -105,10 +105,10 @@ class SynthSignalGen(QMainWindow):
Nt_label = QLabel("# Samples")
self.Nt_edit = QLineEdit()
self.Nt_edit.setStatusTip(
"Number of data points, minimum is 10, maximum is 10 000!"
"Number of data points, minimum is 10, maximum is 25 000!"
)
set_max_width(self.Nt_edit, iwidth)
self.Nt_edit.setValidator(QIntValidator(bottom=10, top=100000))
self.Nt_edit.setValidator(QIntValidator(bottom=10, top=25000))
# --- the basic settings box ---
......@@ -216,12 +216,12 @@ class SynthSignalGen(QMainWindow):
self.alpha_edit.setStatusTip("0 is white noise, must be smaller than 1!")
set_max_width(self.alpha_edit, iwidth)
# does not work as expected :/
V1 = QDoubleValidator()
V1.setNotation(QDoubleValidator.StandardNotation)
V1.setDecimals(200)
V1.setRange(0.000, 0.9999)
V1 = QDoubleValidator(bottom = 0, top = 0.99)
# V1.setNotation(QDoubleValidator.StandardNotation)
# V1.setDecimals(5)
# V1.setRange(0.0, 0.99)
self.alpha_edit.setValidator(V1)
self.alpha_edit.insert("0.2") # initial AR1
self.alpha_edit.insert("0.2") # initial AR(1)
d_label = QLabel("Noise Strength")
self.d_edit = QLineEdit(parent=self.noise_box)
......@@ -967,16 +967,28 @@ class SynthSignalGen(QMainWindow):
# noise
if self.noise_box.isChecked():
# QDoubleValidator is a screw up..
alpha = float(self.alpha_edit.text())
if not 0 < alpha < 1:
try:
# QDoubleValidator is a screw up..
alpha = float(self.alpha_edit.text())
# empty input
except ValueError:
self.OutOfBounds = MessageWindow(
"AR1 parameter must be smaller than 1!", "Value Error"
"Missing AR(1) alpha parameter!", "Value Error"
)
return
if not 0 <= alpha < 1:
self.OutOfBounds = MessageWindow(
"AR1 parameter must be between 0 and <1!", "Value Error"
)
return
# Noise amplitude
if not self.d_edit.hasAcceptableInput():
self.OutOfBounds = MessageWindow(
"Missing noise parameters!", "Value Error"
"Missing noise amplitude!", "Value Error"
)
return
......
pyboat/ui/util.py
View file @ e0849c2c
......@@ -78,7 +78,7 @@ def get_file_path(debug=False):
"""
if debug:
file_names = ['../../data_examples/synth_signals.csv']
file_names = [os.path.join('..', '..', 'data_examples', 'synth_signals.csv')]
pass
# returns a list, stand alone File Dialog
......
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