PGomes92 · PGomes92 · Nov 12, 2019 · Jun 25, 2019 · Jun 30, 2019 · Jun 30, 2019
diff --git a/.gitignore b/.gitignore
@@ -103,3 +103,13 @@ venv.bak/
 # mypy
 .mypy_cache/
 .DS_Store
+docs/Icon
+.idea/workspace.xml
+.idea/vcs.xml
+.idea/pyhrv.iml
+.idea/modules.xml
+.idea/misc.xml
+.idea/markdown-navigator/profiles_settings.xml
+.idea/markdown-navigator.xml
+.idea/dictionaries/pedrogomes.xml
+.idea/codeStyles/codeStyleConfig.xml
diff --git a/.idea/markdown-exported-files.xml b/.idea/markdown-exported-files.xml
diff --git a/LICENSE.txt b/LICENSE.txt
diff --git a/README.md b/README.md
diff --git a/SampleFigures/SampleAR.png b/SampleFigures/SampleAR.png
diff --git a/SampleFigures/SampleDFA.png b/SampleFigures/SampleDFA.png
diff --git a/SampleFigures/SampleECG.png b/SampleFigures/SampleECG.png
diff --git a/SampleFigures/SampleHRHeatplot1.png b/SampleFigures/SampleHRHeatplot1.png
diff --git a/SampleFigures/SampleHRHeatplot2.png b/SampleFigures/SampleHRHeatplot2.png
diff --git a/SampleFigures/SampleHRHeatplot3.png b/SampleFigures/SampleHRHeatplot3.png
diff --git a/SampleFigures/SampleHistogram.png b/SampleFigures/SampleHistogram.png
diff --git a/SampleFigures/SampleLomb.png b/SampleFigures/SampleLomb.png
diff --git a/SampleFigures/SampleNonlinear.png b/SampleFigures/SampleNonlinear.png
diff --git a/SampleFigures/SamplePSDComparisonAR.png b/SampleFigures/SamplePSDComparisonAR.png
diff --git a/SampleFigures/SamplePSDComparisonLomb.png b/SampleFigures/SamplePSDComparisonLomb.png
diff --git a/SampleFigures/SamplePSDComparisonWelch.png b/SampleFigures/SamplePSDComparisonWelch.png
diff --git a/SampleFigures/SamplePSDWaterfallAR.png b/SampleFigures/SamplePSDWaterfallAR.png
diff --git a/SampleFigures/SamplePSDWaterfallLomb.png b/SampleFigures/SamplePSDWaterfallLomb.png
diff --git a/SampleFigures/SamplePSDWaterfallWelch.png b/SampleFigures/SamplePSDWaterfallWelch.png
diff --git a/SampleFigures/SamplePoincare.png b/SampleFigures/SamplePoincare.png
diff --git a/SampleFigures/SampleRadarChart5.png b/SampleFigures/SampleRadarChart5.png
diff --git a/SampleFigures/SampleRadarChart8.png b/SampleFigures/SampleRadarChart8.png
diff --git a/SampleFigures/SampleTachogram.png b/SampleFigures/SampleTachogram.png
diff --git a/SampleFigures/SampleWelch.png b/SampleFigures/SampleWelch.png
diff --git a/SampleFigures/pyhrv.png b/SampleFigures/pyhrv.png
diff --git a/TestData/bittest.csv b/TestData/bittest.csv
diff --git a/TestData/series_1_hrv.txt b/TestData/series_1_hrv.txt
diff --git a/TestData/series_2.npy b/TestData/series_2.npy
diff --git a/TestData/series_2_hrv.txt b/TestData/series_2_hrv.txt
diff --git a/TestData/series_3.npy b/TestData/series_3.npy
diff --git a/TestData/series_3_hrv.txt b/TestData/series_3_hrv.txt
diff --git a/TestData/series_4.npy b/TestData/series_4.npy
diff --git a/TestData/series_4_hrv.txt b/TestData/series_4_hrv.txt
diff --git a/TestData/series_5.npy b/TestData/series_5.npy
diff --git a/TestData/series_5_hrv.txt b/TestData/series_5_hrv.txt
diff --git a/TestData/series_6.npy b/TestData/series_6.npy
diff --git a/TestData/series_7.npy b/TestData/series_7.npy
diff --git a/_gitignore b/_gitignore
@@ -0,0 +1,115 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
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+.installed.cfg
+*.egg
+MANIFEST
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+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
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+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
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+# Django stuff:
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+.python-version
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+*.sage.py
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+.env
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+venv.bak/
+
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+.spyderproject
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+
+# Rope project settings
+.ropeproject
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+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.DS_Store
+docs/Icon
+.idea/workspace.xml
+.idea/vcs.xml
+.idea/pyhrv.iml
+.idea/modules.xml
+.idea/misc.xml
+.idea/markdown-navigator/profiles_settings.xml
+.idea/markdown-navigator.xml
+.idea/dictionaries/pedrogomes.xml
+.idea/codeStyles/codeStyleConfig.xml
diff --git a/changelog.md b/changelog.md
@@ -1,3 +1,88 @@
+Update Version 0.4.0
+--------------------
+#### Major Changes
+- updated hrv_keys.json and fixed some typos
+- added ``modes`` to the Frequency Domain functions ``welch_psd()``, ``ar_psd()``, and ``lomb_psd()`:
+   -	``normal``: Returns frequency domain parameters and PSD plot figure in a ReturnTuple object
+	-	``dev``: Returns frequency domain parameters, frequency and power arrays, no plot figure
+	-	``devplot``: Returns frequency domain parameters, frequency array, power array, and the plot figure
+- Frequency Domain Comparison Features:
+   - added ``pyhrv.frequency_domain.psd_comparison()`` function to plot multiple PSDs (welch, ar, or lomb) from multiple 
+   NNI segments in single plot figure
+
+        **Sample Plots:**
+        [Welch](./SampleFigures/SamplePSDComparisonWelch.png),
+        [Autoregressive](./SampleFigures/SamplePSDComparisonAR.png), and
+        [Lomb-Scargle](./SampleFigures/SamplePSDComparisonLomb.png)     
+        **Docs:**
+        https://pyhrv.readthedocs.io/en/latest/_pages/api/frequency.html#d-psd-comparison-plot-psd-comparison
+   - added ``pyhrv.frequency_domain.psd_waterfall()`` function to plot multiple PSDs (welch, ar, or lomb) from multiple 
+   NNi segments in a 3D Plot (Sample plots: [Welch](./SampleFigures/SamplePSDWaterfallWelch.png), [Autoregressive](
+   ./SampleFigures/SamplePSDWaterfallAR.png), [Lomb](./SampleFigures/SamplePSDWaterfallLomb.png))
+- Added ``pyhrv.tools.heart_rate_heatplot()`` function for graphical visualization & classification of HR performance 
+based on normal HR ranges by age and gender (Sample Plots: [plot 1](./SampleFigures/SampleHRHeatplot1.png), [plot 2](
+./SampleFigures/SampleHRheatplot2), and [plot 3](./SampleFigures/SampleHRHeatplot3.png)).
+- Added ``pyhrv.tools.radar_chart()`` function which plots a radar chart from a series of user-selected HRV parameters 
+based on a
+- removed ``overlap`` input argument from the ``pyhrv.utils.segmentation()`` functions as it had now effect anymore due to the previous updates of this function.
+- ``overlap`` input argument has also been removed from the ``pyhrv.utils.sdnn_index()`` and ``pyhrv.utils.sdann()`` functions for the same reason (both use the ``pyhrv.utils.segmentation()``)
+- Moved, fixed, and improved ``hrv_report()``
+- Overall improved stability of the pyhrv package
+- restructured pyhrv package (see especially ``tools.py`` and the ``utils.py`` modules):
+
+```
+    pyhrv                           # Toolbox
+    ├── files                       # pyHRV support files
+    |   ├── quickstart              # Figures for the quickstart guide (see pyhrv module README.md)
+    |   ├── hr_heatplot.json        # HR reference normal values for the hr_heatplot() function
+    |   ├── hrv_keys.json           # HRV keys to access the parameter results stored in
+    |   ├── references.txt          # Publications references on which pyHRV functions are based
+    |   ├── SampleECG.txt           # Sample ECG signal (for testing purposes)
+    |   ├── SampleExport.json       # Sample HRV results export (for demonstration purposes)
+    |   ├── SampleNNISeriesLong.npy # 60 minute sample NNI series (for testing purposes)
+    |   ├── SampleNNISeriesShort.npy# 5 minute sample NNI series (for testing purposes)
+    |   ├── SampleReport.csv        # Sample report in .csv format
+    |   ├── SampleReport.pdf        # Sample report in .pdf format
+    |   └── SampleReport.txt        # Sample report in .txt format
+    |      
+    ├── report                      # Subpackage for PDF, TXT, and CSV report generation
+    |   ├── build                   # Default path for generated PDF, TXT, and CSV reports 
+    |   ├── figure                  # Working directory where figures for the PDF report are temporarily stored
+    |   ├── templates               # LaTeX templates for the PDF reports (feel free to customize)
+    |   ├── __init__.py             # Report init file
+    |   ├── main.tex                # Main LaTeX file
+    |   ├── parameters.tex          # File containing all the variables in which the HRV parameters will be stored
+    |   ├── pyhrv.png               # pyHRV logo for the PDF header
+    |   ├── README.md               # Report README
+    |   └── settings.tex            # Settings file for the LaTeX-based project
+    |   
+    ├── __init__.py                 # pyHRV init file
+    ├── __version__.py              # pyHRV version
+    ├── hrv.py                      # HRV function
+    ├── frequency_domain_.py        # Frequency Domain functions
+    ├── nonlinear.py                # Nonlinear Parameters functions
+    ├── time_domain.py              # Time Domain functions
+    ├── tools.py                    # HRV tools functions (Tachogram, ECG, radar chart, HR heatplot, and other 
+    |                               # Comparison functions
+    └── utils.py                    # General data verification, conversion, file handling, etc.
+
+```
+
+- the ``tools.py`` now only contains tools specifically designed for HRV analysis (support)
+- the ``utils.py`` now only contains support functions required for the computation of the tools and computation of 
+HRV parameters
+
+#### Minor Changes
+- pyhrv.nonlinear.dfa(): added ``dfa_alpha1_beats`` return key with short term fluctuation and ``dfa_alpha2_beats` return key with long term fluctuation values
+- updated hrv_keys.json file
+- added ``complete`` as valid value for the ``interval`` input parameter of the ``tools.plot_ecg`` and ``tools
+.tachogram``
+functions
+- pyhrv.time_domain.tinn() & pyhrv.time_domain.geometrical_parameters() functions no issue a warning due to the current issue of the TINN function of providing wrong results (see issue #5)
+- removed 'overlap' input parameter from ``sdnn`` and ``sdnn_index`` functions 
+- updated main README
+- Fixes #6, #7 and #9
+
 Update Version 0.3.2
 --------------------
 - IMPORTANT: fixes installation issues under Python3 using pip install (full support must yet be tested)

diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/make.bat b/docs/make.bat