Readme (#86)

* Update README.md

removed last remnant of old name on this branch

* Create artwork

* Add files via upload

* Update ver3 zoo2.svg

* Update ver3 zoo2.svg

* Delete ver3 zoo2.svg

* Delete ver3 zoo3.svg

* Delete ver3 zoo5.svg

* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Create IsoAutio.svg

* Delete ver3_zoo8.svg

* Delete ver3_zoo5.svg

* Delete ver3_zoo1.svg

* Delete ver3_zoo2.svg

* Delete ver2.svg

* Delete ver1.svg

* Create PyHa

* Rename PyHa to PyHa.svg

* Delete ver3_zoo3.svg

* Delete ver3_zoo7.svg

* Delete artwork

* Created separate folder for conda environments, added Ubuntu 18.04 environment

* Removing old Ubuntu 16.04 environment

No longer needed since the last commit added the conda_environments folder

* Added in a Windows 10 environment file

Tested on one machine

* Add files via upload

Adding environment .yml file for macOS Big Sur 11.4

* isolate function

* Update README.md

* isolation_parameters

* threshold function

* return values

* Update README.md

* Update README.md

* usage

* file links

* Locations

* isolation_parameters update

* isolation_parameters update

* design

* Update README.md

* Update README.md

* steinberg_isolate

* Table of Contents

* PyHa Logo

* logo

* steinberg isolate

* update logo

* steinberg isolate

* isolation techniques

* rename variables

* generate_automated_labels

* generate_automated_labels

* kaleidoscope_conversion

* All IsoAudio.py files

* section headings

* local_line_graph

* local_score_visualization

* plot_bird_label_scores

* All visualizations.py functions

* comments

* microfaune_package notes

* annotation_duration_statistics

* bird_label_scores

* automated_labeling_statistics

* global_dataset_statistics

* clip_IOU

* matrix_IoU_Scores

* clip_catch

* global_IOU_Statistics

* dataset_Catch

* dataset_IoU_Statistics

* All statistics.py functions

* Sections

* sections

* update dataset_IoU_Statistics

* Update image

* Formatting

* Update Image

* Update installation directions

* change to numbered list

* Update Installation Directions

* Update README.md

* Examples, Remove "How it Works"

* Update README.md

* Update README.md

* isolation params in example

* Examples

* Update Graphs

* Update Style

* Credit

* Credit update

* Credits updates

* Update README.md

removed "Install Jupyter Notebook" step
This should be accomplished by the conda environment install.

* Update README.md

Adjusted Examples portion. Results were created and pushed from my Linux Mint laptop which is built off of Ubuntu 16.04

* Update Readme.md with relevant Screaming Piha Test set information

Would be smart to get someone that is new with PyHa to see if they can easily get things up and running simply by reading the readme. I also added in more details to the steps to make them more foolproof, might be overkill.

* Updated Images

Co-authored-by: Jacob <jgayers@ucsd.edu>
Co-authored-by: NathalieFranklin <69173439+NathalieFranklin@users.noreply.github.com>
Co-authored-by: Jacob <jacobthescreenwriter@gmail.com>
Co-authored-by: mugen13lue <33683103+mugen13lue@users.noreply.github.com>

conda_environments/environment_MacOS_BigSur.11.4.yml

@@ -0,0 +1,202 @@
+name: species-id
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - absl-py=0.12.0=pyhd8ed1ab_0
+  - appdirs=1.4.4=pyh9f0ad1d_0
+  - argon2-cffi=20.1.0=py37hf967b71_2
+  - astor=0.8.1=pyh9f0ad1d_0
+  - async_generator=1.10=py_0
+  - attrs=20.3.0=pyhd3deb0d_0
+  - audioread=2.1.9=py37hf985489_0
+  - backcall=0.2.0=pyh9f0ad1d_0
+  - backports=1.0=py_2
+  - backports.functools_lru_cache=1.6.3=pyhd8ed1ab_0
+  - bleach=3.3.0=pyh44b312d_0
+  - brotlipy=0.7.0=py37hf967b71_1001
+  - bzip2=1.0.8=h0d85af4_4
+  - c-ares=1.17.1=h0d85af4_1
+  - ca-certificates=2020.12.5=h033912b_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - certifi=2020.12.5=py38h50d1736_1
+  - cffi=1.14.5=py37h4d371b4_0
+  - chardet=4.0.0=py39h6e9494a_1
+  - cryptography=3.4.7=py38h1fa4640_0
+  - cycler=0.10.0=py_2
+  - dbus=1.13.6=ha13b53f_2
+  - decorator=5.0.6=pyhd8ed1ab_0
+  - defusedxml=0.7.1=pyhd8ed1ab_0
+  - entrypoints=0.3=pyhd8ed1ab_1003
+  - expat=2.3.0=he49afe7_0
+  - ffmpeg=4.3.1=hb787a4c_2
+  - fontconfig=2.13.1=hd23ceaa_1004
+  - freetype=2.10.4=h4cff582_1
+  - gast=0.4.0=pyh9f0ad1d_0
+  - gettext=0.19.8.1=h7937167_1005
+  - glib=2.68.1=he49afe7_0
+  - glib-tools=2.68.1=he49afe7_0
+  - gmp=6.2.1=h2e338ed_0
+  - gnutls=3.6.13=h756fd2b_1
+  - google-pasta=0.2.0=pyh8c360ce_0
+  - grpcio=1.37.0=py36h8d587b5_0
+  - gst-plugins-base=1.18.4=h63a84d5_1
+  - gstreamer=1.18.4=h8622b34_0
+  - h5py=2.10.0=nompi_py38h9a16e60_106
+  - hdf5=1.10.6=nompi_hc5d9132_1114
+  - icu=68.1=h74dc148_0
+  - idna=2.10=pyh9f0ad1d_0
+  - importlib-metadata=3.10.0=py39h6e9494a_0
+  - ipykernel=5.5.3=py38h6c79ece_0
+  - ipython=7.22.0=py38h6c79ece_0
+  - ipython_genutils=0.2.0=py_1
+  - ipywidgets=7.6.3=pyhd3deb0d_0
+  - jedi=0.18.0=py39h6e9494a_2
+  - jinja2=2.11.3=pyh44b312d_0
+  - joblib=1.0.1=pyhd8ed1ab_0
+  - jpeg=9d=hbcb3906_0
+  - jsonschema=3.2.0=pyhd8ed1ab_3
+  - jupyter=1.0.0=py39h6e9494a_6
+  - jupyter_client=6.1.12=pyhd8ed1ab_0
+  - jupyter_console=6.4.0=pyhd8ed1ab_0
+  - jupyter_core=4.7.1=py37hf985489_0
+  - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
+  - jupyterlab_widgets=1.0.0=pyhd8ed1ab_1
+  - keras-applications=1.0.8=py_1
+  - keras-preprocessing=1.1.2=pyhd8ed1ab_0
+  - kiwisolver=1.3.1=py36h615c93b_1
+  - krb5=1.17.2=h60d9502_0
+  - lame=3.100=h35c211d_1001
+  - lcms2=2.12=h577c468_0
+  - ld_impl_linux-64=2.35.1=h8edb8f9_2
+  - libblas=3.9.0=8_openblas
+  - libcblas=3.9.0=8_openblas
+  - libclang=11.1.0=default_he082bbe_0
+  - libcurl=7.76.0=h8ef9fac_0
+  - libedit=3.1.20191231=h0678c8f_2
+  - libev=4.33=haf1e3a3_1
+  - libevent=2.1.10=hddc9c9b_3
+  - libffi=3.3=h046ec9c_2
+  - libflac=1.3.3=h74dc148_1
+  - libgfortran5=9.3.0=h6c81a4c_17
+  - libglib=2.68.1=hd556434_0
+  - libiconv=1.16=haf1e3a3_0
+  - liblapack=3.9.0=8_openblas
+  - libllvm10=10.0.1=h009f743_3
+  - libllvm11=11.1.0=hd011deb_2
+  - libnghttp2=1.43.0=h07e645a_0
+  - libogg=1.3.4=h35c211d_1
+  - libopenblas=0.3.12=openmp_h63d9170_1
+  - libopus=1.3.1=hc929b4f_1
+  - libpng=1.6.37=h7cec526_2
+  - libpq=13.1=h052a64a_2
+  - libprotobuf=3.15.7=hcf210ce_0
+  - librosa=0.8.0=pyh9f0ad1d_0
+  - libsndfile=1.0.31=he49afe7_1
+  - libsodium=1.0.18=hbcb3906_1
+  - libssh2=1.9.0=h52ee1ee_6
+  - libtiff=4.2.0=h355d032_0
+  - libuuid=2.32.1=h35c211d_1000
+  - libvorbis=1.3.7=h046ec9c_0
+  - libwebp-base=1.2.0=h0d85af4_2
+  - libxcb=1.13=h35c211d_1003
+  - libxml2=2.9.10=h802ca4f_3
+  - llvmlite=0.36.0=py38h872f124_0
+  - lz4-c=1.9.3=h046ec9c_0
+  - markdown=3.3.4=pyhd8ed1ab_0
+  - markupsafe=1.1.1=py37hf967b71_3
+  - matplotlib-base=3.4.1=py39hb07454d_0
+  - mistune=0.8.4=py37hf967b71_1003
+  - mysql-common=8.0.23=h694c41f_1
+  - mysql-libs=8.0.23=h54f5a68_2
+  - nbclient=0.5.3=pyhd8ed1ab_0
+  - nbconvert=6.0.7=py38h50d1736_3
+  - nbformat=5.1.3=pyhd8ed1ab_0
+  - ncurses=6.2=h2e338ed_4
+  - nest-asyncio=1.5.1=pyhd8ed1ab_0
+  - nettle=3.6=hedd7734_0
+  - notebook=6.3.0=py37h5186d4c_0
+  - nspr=4.30=hcd9eead_0
+  - nss=3.63=h31e2bf1_0
+  - numba=0.53.1=py38h8fd2267_0
+  - numpy=1.20.2=py39h7eed0ac_0
+  - olefile=0.46=pyh9f0ad1d_1
+  - openh264=2.1.1=hfd3ada9_0
+  - openjpeg=2.4.0=h6cbf5cd_0
+  - openssl=1.1.1k=h0d85af4_0
+  - packaging=20.9=pyh44b312d_0
+  - pandas=1.2.3=py39h4d6be9b_0
+  - pandoc=2.12=h0d85af4_0
+  - pandocfilters=1.4.2=py36_0
+  - parso=0.8.2=pyhd8ed1ab_0
+  - pcre=8.44=h4a8c4bd_0
+  - pexpect=4.8.0=pyh9f0ad1d_2
+  - pickleshare=0.7.5=py_1003
+  - pillow=8.1.2=py38h83525de_1
+  - pip=21.0.1=pyhd8ed1ab_0
+  - pooch=1.3.0=pyhd8ed1ab_0
+  - prometheus_client=0.10.1=pyhd8ed1ab_0
+  - prompt-toolkit=3.0.18=pyha770c72_0
+  - prompt_toolkit=3.0.18=hd8ed1ab_0
+  - protobuf=3.15.7=py39h9fcab8e_0
+  - pthread-stubs=0.4=hc929b4f_1001
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - pycparser=2.20=pyh9f0ad1d_2
+  - pygments=2.8.1=pyhd8ed1ab_0
+  - pyopenssl=20.0.1=pyhd8ed1ab_0
+  - pyparsing=2.4.7=pyh9f0ad1d_0
+  - pyqt=5.12.3=py38h50d1736_7
+  - pyqt-impl=5.12.3=py38h721a93c_7
+  - pyqt5-sip=4.19.18=py38h5745d40_7
+  - pyqtchart=5.12=py38h721a93c_7
+  - pyqtwebengine=5.12.1=py38h721a93c_7
+  - pyrsistent=0.17.3=py37hf967b71_2
+  - pysocks=1.7.1=py38h50d1736_3
+  - pysoundfile=0.10.3.post1=pyhd3deb0d_0
+  - python=3.7.10=h7728216_100_cpython
+  - python-dateutil=2.8.1=py_0
+  - python_abi=3.7=1_cp37m
+  - pytz=2021.1=pyhd8ed1ab_0
+  - pyzmq=22.0.3=py38hd3b92b6_1
+  - qt=5.12.9=h126340a_4
+  - qtconsole=5.0.3=pyhd8ed1ab_0
+  - qtpy=1.9.0=py_0
+  - readline=8.0=h0678c8f_2
+  - requests=2.25.1=pyhd3deb0d_0
+  - resampy=0.2.2=py_0
+  - scikit-learn=0.24.1=py38hfd19401_0
+  - scipy=1.6.2=py38h431c0a8_0
+  - send2trash=1.5.0=py_0
+  - setuptools=49.6.0=py38h50d1736_3
+  - six=1.15.0=pyh9f0ad1d_0
+  - sqlite=3.35.4=h44b9ce1_0
+  - tensorboard=1.14.0=py37_0
+  - tensorflow=1.14.0=h3cdfc77_0
+  - tensorflow-base=1.14.0=mkl_py37h5a24fda_0
+  - tensorflow-estimator=1.14.0=py37h5ca1d4c_0
+  - termcolor=1.1.0=py_2
+  - terminado=0.9.4=py37hf985489_0
+  - testpath=0.4.4=py_0
+  - threadpoolctl=2.1.0=pyh5ca1d4c_0
+  - tk=8.6.10=h0419947_1
+  - tornado=6.1=py37hf967b71_1
+  - traitlets=5.0.5=py_0
+  - typing_extensions=3.7.4.3=py_0
+  - urllib3=1.26.4=pyhd8ed1ab_0
+  - wcwidth=0.2.5=pyh9f0ad1d_2
+  - webencodings=0.5.1=py_1
+  - werkzeug=1.0.1=pyh9f0ad1d_0
+  - wheel=0.36.2=pyhd3deb0d_0
+  - widgetsnbextension=3.5.1=py37hf985489_4
+  - wrapt=1.12.1=py36h20b66c6_3
+  - x264=1!161.3030=h35c211d_0
+  - xorg-libxau=1.0.9=h35c211d_0
+  - xorg-libxdmcp=1.1.3=h35c211d_0
+  - xz=5.2.5=h0b31af3_1
+  - zeromq=4.3.4=h1c7c35f_0
+  - zipp=3.4.1=pyhd8ed1ab_0
+  - zlib=1.2.11=h7795811_1010
+  - zstd=1.4.9=h582d3a0_0
+prefix: /home/jacob/miniconda3/envs/species-id
+