From 15689e13ea9ecb7c1874f0d437c2881d01f5f0dc Mon Sep 17 00:00:00 2001
From: Ian Liu <37123262+Ianyliu@users.noreply.github.com>
Date: Tue, 10 Sep 2024 09:52:03 -0400
Subject: [PATCH 1/4] Update requirements.txt

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index c25f100..628e7b2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ matplotlib>=2.0.0
 vtk>=8.1.0
 nibabel
 pillow
-pandas
+pandas<=1.3.0
 scipy>=0.17.0
 scikit-learn>=0.22.0
 nilearn

From 256bdaaf226d262c09c3ed7f6f1cb427d6dda7b1 Mon Sep 17 00:00:00 2001
From: Ian Liu <37123262+Ianyliu@users.noreply.github.com>
Date: Tue, 10 Sep 2024 09:52:50 -0400
Subject: [PATCH 2/4] Add Conda Env File

---
 environment.yml | 258 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 258 insertions(+)
 create mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..ae32214
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,258 @@
+name: enigma
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - aiohappyeyeballs=2.4.0=pyhd8ed1ab_0
+  - aiohttp=3.10.5=py38h3237794_0
+  - aiosignal=1.3.1=pyhd8ed1ab_0
+  - anyio=3.7.1=pyhd8ed1ab_0
+  - aom=3.9.1=h7bae524_0
+  - appnope=0.1.4=pyhd8ed1ab_0
+  - asttokens=2.4.1=pyhd8ed1ab_0
+  - async-timeout=4.0.3=pyhd8ed1ab_0
+  - attrs=24.2.0=pyh71513ae_0
+  - backcall=0.2.0=pyh9f0ad1d_0
+  - bleach=6.1.0=pyhd8ed1ab_0
+  - blosc=1.21.6=h5499902_0
+  - bokeh=2.4.3=pyhd8ed1ab_3
+  - brotli=1.1.0=hb547adb_1
+  - brotli-bin=1.1.0=hb547adb_1
+  - brotli-python=1.1.0=py38he333c0f_1
+  - bzip2=1.0.8=h99b78c6_7
+  - c-ares=1.33.1=hd74edd7_0
+  - ca-certificates=2024.8.30=hf0a4a13_0
+  - cairo=1.18.0=hb4a6bf7_3
+  - certifi=2024.8.30=pyhd8ed1ab_0
+  - cffi=1.17.0=py38h858044d_0
+  - charset-normalizer=3.3.2=pyhd8ed1ab_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - comm=0.2.2=pyhd8ed1ab_0
+  - contourpy=1.1.1=py38h9afee92_1
+  - cycler=0.12.1=pyhd8ed1ab_0
+  - dav1d=1.2.1=hb547adb_0
+  - debugpy=1.8.5=py38h11842c7_0
+  - decorator=5.1.1=pyhd8ed1ab_0
+  - double-conversion=3.3.0=h13dd4ca_0
+  - eigen=3.4.0=h1995070_0
+  - exceptiongroup=1.2.2=pyhd8ed1ab_0
+  - executing=2.1.0=pyhd8ed1ab_0
+  - expat=2.6.3=hf9b8971_0
+  - ffmpeg=6.1.2=gpl_h3ef3969_102
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=h77eed37_2
+  - fontconfig=2.14.2=h82840c6_0
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - fonttools=4.53.1=py38h3237794_0
+  - freetype=2.12.1=hadb7bae_2
+  - fribidi=1.0.10=h27ca646_0
+  - frozenlist=1.4.1=py38h336bac9_0
+  - gettext=0.22.5=h8414b35_3
+  - gettext-tools=0.22.5=h8414b35_3
+  - git=2.46.0=pl5321h41514c7_0
+  - gl2ps=1.4.2=hc97c1ff_1
+  - glew=2.1.0=h9f76cd9_2
+  - gmp=6.3.0=h7bae524_2
+  - gnutls=3.8.7=h9df781c_0
+  - graphite2=1.3.13=hebf3989_1003
+  - h2=4.1.0=pyhd8ed1ab_0
+  - harfbuzz=9.0.0=h997cde5_1
+  - hdf4=4.2.15=h2ee6834_7
+  - hdf5=1.14.3=nompi_hec07895_105
+  - hpack=4.0.0=pyh9f0ad1d_0
+  - hyperframe=6.0.1=pyhd8ed1ab_0
+  - icu=75.1=hfee45f7_0
+  - idna=3.8=pyhd8ed1ab_0
+  - importlib-metadata=8.4.0=pyha770c72_0
+  - importlib-resources=6.4.5=pyhd8ed1ab_0
+  - importlib_metadata=8.4.0=hd8ed1ab_0
+  - importlib_resources=6.4.5=pyhd8ed1ab_0
+  - ipykernel=6.29.5=pyh57ce528_0
+  - ipython=8.12.0=pyhd1c38e8_0
+  - jedi=0.19.1=pyhd8ed1ab_0
+  - jinja2=3.1.4=pyhd8ed1ab_0
+  - joblib=1.4.2=pyhd8ed1ab_0
+  - jsoncpp=1.9.5=hc021e02_1
+  - jupyter_client=8.6.2=pyhd8ed1ab_0
+  - jupyter_core=5.7.2=py38h10201cd_0
+  - kiwisolver=1.4.5=py38h9afee92_1
+  - krb5=1.21.3=h237132a_0
+  - lame=3.100=h1a8c8d9_1003
+  - lcms2=2.16=ha0e7c42_0
+  - lerc=4.0.0=h9a09cb3_0
+  - libabseil=20240116.2=cxx17_h00cdb27_1
+  - libaec=1.1.3=hebf3989_0
+  - libasprintf=0.22.5=h8414b35_3
+  - libasprintf-devel=0.22.5=h8414b35_3
+  - libass=0.17.3=hf20b609_0
+  - libblas=3.9.0=20_osxarm64_openblas
+  - libbrotlicommon=1.1.0=hb547adb_1
+  - libbrotlidec=1.1.0=hb547adb_1
+  - libbrotlienc=1.1.0=hb547adb_1
+  - libcblas=3.9.0=20_osxarm64_openblas
+  - libclang-cpp16=16.0.6=default_h5c12605_13
+  - libclang13=18.1.8=default_hfc66aa2_4
+  - libcurl=8.9.1=hfd8ffcc_0
+  - libcxx=18.1.8=h3ed4263_7
+  - libdeflate=1.21=h99b78c6_0
+  - libedit=3.1.20191231=hc8eb9b7_2
+  - libev=4.33=h93a5062_2
+  - libexpat=2.6.3=hf9b8971_0
+  - libffi=3.4.2=h3422bc3_5
+  - libgettextpo=0.22.5=h8414b35_3
+  - libgettextpo-devel=0.22.5=h8414b35_3
+  - libgfortran=5.0.0=13_2_0_hd922786_3
+  - libgfortran5=13.2.0=hf226fd6_3
+  - libglib=2.80.3=h59d46d9_2
+  - libhwloc=2.11.1=default_h7685b71_1000
+  - libiconv=1.17=h0d3ecfb_2
+  - libidn2=2.3.7=h93a5062_0
+  - libintl=0.22.5=h8414b35_3
+  - libintl-devel=0.22.5=h8414b35_3
+  - libjpeg-turbo=3.0.0=hb547adb_1
+  - liblapack=3.9.0=20_osxarm64_openblas
+  - libllvm16=16.0.6=haab561b_3
+  - libllvm18=18.1.8=h5090b49_2
+  - libnetcdf=4.9.2=nompi_he469be0_114
+  - libnghttp2=1.58.0=ha4dd798_1
+  - libogg=1.3.5=h99b78c6_0
+  - libopenblas=0.3.25=openmp_h6c19121_0
+  - libopenvino=2024.3.0=h5c9529b_0
+  - libopenvino-arm-cpu-plugin=2024.3.0=h5c9529b_0
+  - libopenvino-auto-batch-plugin=2024.3.0=hcd65546_0
+  - libopenvino-auto-plugin=2024.3.0=hcd65546_0
+  - libopenvino-hetero-plugin=2024.3.0=h88cb26a_0
+  - libopenvino-ir-frontend=2024.3.0=h88cb26a_0
+  - libopenvino-onnx-frontend=2024.3.0=h32b5460_0
+  - libopenvino-paddle-frontend=2024.3.0=h32b5460_0
+  - libopenvino-pytorch-frontend=2024.3.0=h00cdb27_0
+  - libopenvino-tensorflow-frontend=2024.3.0=h2741c3b_0
+  - libopenvino-tensorflow-lite-frontend=2024.3.0=h00cdb27_0
+  - libopus=1.3.1=h27ca646_1
+  - libpng=1.6.43=h091b4b1_0
+  - libpq=16.4=h671472c_1
+  - libprotobuf=4.25.3=hbfab5d5_0
+  - libsodium=1.0.18=h27ca646_1
+  - libsqlite=3.46.1=hc14010f_0
+  - libssh2=1.11.0=h7a5bd25_0
+  - libtasn1=4.19.0=h1a8c8d9_0
+  - libtheora=1.1.1=h99b78c6_1006
+  - libtiff=4.6.0=hf8409c0_4
+  - libunistring=0.9.10=h3422bc3_0
+  - libvorbis=1.3.7=h9f76cd9_0
+  - libvpx=1.14.1=h7bae524_0
+  - libwebp-base=1.4.0=h93a5062_0
+  - libxcb=1.16=hc9fafa5_1
+  - libxml2=2.12.7=h01dff8b_4
+  - libxslt=1.1.39=h223e5b9_0
+  - libzip=1.10.1=ha0bc3c6_3
+  - libzlib=1.3.1=hfb2fe0b_1
+  - llvm-openmp=18.1.8=hde57baf_1
+  - loguru=0.7.2=py38h10201cd_1
+  - lxml=5.3.0=py38hdedcbec_0
+  - lz4-c=1.9.4=hb7217d7_0
+  - markdown=3.6=pyhd8ed1ab_0
+  - markupsafe=2.1.5=py38h336bac9_0
+  - matplotlib=3.7.3=py38h150bfb4_0
+  - matplotlib-base=3.7.3=py38hef9d0d7_0
+  - matplotlib-inline=0.1.7=pyhd8ed1ab_0
+  - msgpack-python=1.0.8=py38h4b8c310_0
+  - multidict=6.0.5=py38hb991d35_0
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - mysql-common=9.0.1=h1687695_0
+  - mysql-libs=9.0.1=h0e80b4a_0
+  - ncurses=6.5=h7bae524_1
+  - nest-asyncio=1.6.0=pyhd8ed1ab_0
+  - nettle=3.9.1=h40ed0f5_0
+  - nibabel=5.2.1=pyha770c72_0
+  - nilearn=0.10.4=pyhd8ed1ab_0
+  - nlohmann_json=3.11.3=h00cdb27_1
+  - numpy=1.24.4=py38ha84db1f_0
+  - openh264=2.4.1=hebf3989_0
+  - openjpeg=2.5.2=h9f1df11_0
+  - openssl=3.3.2=h8359307_0
+  - p11-kit=0.24.1=h29577a5_0
+  - packaging=24.1=pyhd8ed1ab_0
+  - pandas=1.3.0=py38h3777fb4_0
+  - panel=0.14.0=pyhd8ed1ab_0
+  - param=1.13.0=pyh1a96a4e_0
+  - parso=0.8.4=pyhd8ed1ab_0
+  - pcre2=10.44=h297a79d_2
+  - perl=5.32.1=7_h4614cfb_perl5
+  - pexpect=4.9.0=pyhd8ed1ab_0
+  - pickleshare=0.7.5=py_1003
+  - pillow=10.4.0=py38h2c6aaed_0
+  - pip=24.2=pyh8b19718_1
+  - pixman=0.43.4=hebf3989_0
+  - platformdirs=4.3.2=pyhd8ed1ab_0
+  - pooch=1.8.2=pyhd8ed1ab_0
+  - proj=9.4.1=hfb94cee_1
+  - prompt-toolkit=3.0.47=pyha770c72_0
+  - prompt_toolkit=3.0.47=hd8ed1ab_0
+  - psutil=6.0.0=py38h3237794_0
+  - pthread-stubs=0.4=h27ca646_1001
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - pugixml=1.14=h13dd4ca_0
+  - pure_eval=0.2.3=pyhd8ed1ab_0
+  - pycparser=2.22=pyhd8ed1ab_0
+  - pyct=0.5.0=py38hca03da5_0
+  - pygments=2.18.0=pyhd8ed1ab_0
+  - pyparsing=3.1.4=pyhd8ed1ab_0
+  - pysocks=1.7.1=pyha2e5f31_6
+  - python=3.8.19=h2469fbe_0_cpython
+  - python-dateutil=2.9.0=pyhd8ed1ab_0
+  - python_abi=3.8=5_cp38
+  - pytz=2024.1=pyhd8ed1ab_0
+  - pyviz_comms=3.0.3=pyhd8ed1ab_0
+  - pyyaml=6.0.2=py38h3237794_0
+  - pyzmq=26.2.0=py38h7e0d939_0
+  - qt6-main=6.7.2=h4682d5d_5
+  - readline=8.2=h92ec313_1
+  - requests=2.32.3=pyhd8ed1ab_0
+  - scikit-learn=1.3.2=py38he1bc1c9_2
+  - scipy=1.10.1=py38h038e806_3
+  - setuptools=59.8.0=py38h10201cd_1
+  - six=1.16.0=pyh6c4a22f_0
+  - snappy=1.2.1=hd02b534_0
+  - sniffio=1.3.1=pyhd8ed1ab_0
+  - sqlite=3.46.1=h3b4c4e4_0
+  - stack_data=0.6.2=pyhd8ed1ab_0
+  - svt-av1=2.2.1=ha39b806_0
+  - tbb=2021.13.0=h7b3277c_0
+  - tbb-devel=2021.13.0=h8e01b61_0
+  - threadpoolctl=3.5.0=pyhc1e730c_0
+  - tk=8.6.13=h5083fa2_1
+  - tornado=6.4.1=py38h3237794_0
+  - tqdm=4.66.5=pyhd8ed1ab_0
+  - traitlets=5.14.3=pyhd8ed1ab_0
+  - typing-extensions=4.12.2=hd8ed1ab_0
+  - typing_extensions=4.12.2=pyha770c72_0
+  - unicodedata2=15.1.0=py38hb192615_0
+  - urllib3=2.2.2=pyhd8ed1ab_1
+  - utfcpp=4.0.5=hce30654_0
+  - vtk=9.3.1=qt_py38h07c347a_204
+  - vtk-base=9.3.1=qt_py38h9391cbe_204
+  - vtk-io-ffmpeg=9.3.1=qt_py38h64321a6_204
+  - watchfiles=0.21.0=py38hf0e4da2_0
+  - wcwidth=0.2.13=pyhd8ed1ab_0
+  - webencodings=0.5.1=pyhd8ed1ab_2
+  - wheel=0.44.0=pyhd8ed1ab_0
+  - wslink=2.1.3=pyhd8ed1ab_0
+  - x264=1!164.3095=h57fd34a_2
+  - x265=3.5=hbc6ce65_3
+  - xorg-libxau=1.0.11=hb547adb_0
+  - xorg-libxdmcp=1.1.3=h27ca646_0
+  - xz=5.2.6=h57fd34a_0
+  - yaml=0.2.5=h3422bc3_2
+  - yarl=1.9.4=py38h336bac9_0
+  - zeromq=4.3.5=hcc0f68c_4
+  - zipp=3.20.1=pyhd8ed1ab_0
+  - zlib=1.3.1=hfb2fe0b_1
+  - zstandard=0.23.0=py38h43bb1b3_0
+  - zstd=1.5.6=hb46c0d2_0
+  - pip:
+      # - enigmatoolbox==2.0.3
+      - git+https://github.com/MICA-MNI/ENIGMA.git
\ No newline at end of file

From e33861720ecbfca379552e3cba3cca813fb4b213 Mon Sep 17 00:00:00 2001
From: Ian Liu <37123262+Ianyliu@users.noreply.github.com>
Date: Tue, 10 Sep 2024 13:47:24 -0400
Subject: [PATCH 3/4] reolve JupyteNotebook display error

---
 enigmatoolbox/plotting/base.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/enigmatoolbox/plotting/base.py b/enigmatoolbox/plotting/base.py
index 73cf978..51ddcaa 100644
--- a/enigmatoolbox/plotting/base.py
+++ b/enigmatoolbox/plotting/base.py
@@ -410,7 +410,12 @@ def to_notebook(self, transparent_bg=True, scale=(1, 1)):
         wimg = self._win2img(transparent_bg, scale)
         writer = BSPNGWriter(writeToMemory=True)
         result = serial_connect(wimg, writer, as_data=False).result
-        data = memoryview(result).tobytes()
+  
+        try:
+            data = memoryview(result).tobytes()
+        except Exception as e:
+            print(e)
+            data = memoryview(result.VTKObject).tobytes()
         from IPython.display import Image
         return Image(data)
 

From 105fcc60ab8c0f4e2897d9aa55fde44d77536287 Mon Sep 17 00:00:00 2001
From: Ian Liu <37123262+Ianyliu@users.noreply.github.com>
Date: Fri, 20 Dec 2024 22:53:53 -0500
Subject: [PATCH 4/4] Update requirements.txt

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 628e7b2..acf908b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 numpy>=1.11.0
 matplotlib>=2.0.0
-vtk>=8.1.0
+vtk>=8.1.0, <9.4.0
 nibabel
 pillow
 pandas<=1.3.0