Update environment GIT, fix bad reference in bibtex. Add batch for in…

…stallation
geoscixyz · Oct 26, 2018 · ac6699b · ac6699b
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commit ac6699b
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Showing 14 changed files with 58 additions and 992 deletions.
diff --git a/Install_Environment.bat b/Install_Environment.bat
@@ -0,0 +1 @@
+conda env create -f environment.yml
diff --git a/Notebooks/2_1_1_a_Synthetic_Mag_Data_Profile.ipynb b/Notebooks/2_1_1_a_Synthetic_Mag_Data_Profile.ipynb
@@ -22,39 +22,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "0dea334bc95a4285b4ad16f69f613f14",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/html": [
-       "<p>Failed to display Jupyter Widget of type <code>interactive</code>.</p>\n",
-       "<p>\n",
-       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
-       "  that the widgets JavaScript is still loading. If this message persists, it\n",
-       "  likely means that the widgets JavaScript library is either not installed or\n",
-       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
-       "  Widgets Documentation</a> for setup instructions.\n",
-       "</p>\n",
-       "<p>\n",
-       "  If you're reading this message in another frontend (for example, a static\n",
-       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
-       "  it may mean that your frontend doesn't currently support widgets.\n",
-       "</p>\n"
-      ],
-      "text/plain": [
-       "interactive(children=(FloatSlider(value=-7.536722527700476, continuous_update=False, description='East', max=2517.4632774722995, min=-2532.5367225277005, step=10.0), FloatSlider(value=-41.0773809524253, continuous_update=False, description='North', max=2733.9226190475747, min=-2816.0773809524253, step=10.0), FloatSlider(value=90.0, continuous_update=False, description='Azimuth', max=180.0, step=5.0), FloatSlider(value=1875.916442702073, continuous_update=False, description='Length', max=3751.832885404146, min=20.0, step=20.0), BoundedFloatText(value=100.0, description='Sampling', max=1000.0, min=10.0, step=5.0), Output()), _dom_classes=('widget-interact',))"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "## Load all libraries and setup the synthetic problem\n",
     "from GeoToolkit.Mag import Simulator, DataIO\n",

diff --git a/Notebooks/2_1_1_b_Synthetic_Mag_Data_Mag_Field.ipynb b/Notebooks/2_1_1_b_Synthetic_Mag_Data_Mag_Field.ipynb
@@ -23,7 +23,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,39 +41,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f78be9ebe3084cd7bb26340496288cbc",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/html": [
-       "<p>Failed to display Jupyter Widget of type <code>interactive</code>.</p>\n",
-       "<p>\n",
-       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
-       "  that the widgets JavaScript is still loading. If this message persists, it\n",
-       "  likely means that the widgets JavaScript library is either not installed or\n",
-       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
-       "  Widgets Documentation</a> for setup instructions.\n",
-       "</p>\n",
-       "<p>\n",
-       "  If you're reading this message in another frontend (for example, a static\n",
-       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
-       "  it may mean that your frontend doesn't currently support widgets.\n",
-       "</p>\n"
-      ],
-      "text/plain": [
-       "interactive(children=(Dropdown(description='Location:', options=('North Pole', 'Yukon', 'Northern BC', 'Montreal', 'Nevada', 'Mexico', 'Colombia', 'Peru', 'Chile', 'South Africa', 'Serbia', 'Turkey', 'Delhi', 'Beijing', 'Brisbane', 'South Pole'), value='North Pole'), Output()), _dom_classes=('widget-interact',))"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "view = Simulator.worldViewerWidget(worldFile, sites, dataGrid, shapeFile='./assets/Synthetic/Synthetic_Zcontours.shp')\n",
     "display(view)"

diff --git a/Notebooks/2_1_2_Synthetic_Data_Gridding.ipynb b/Notebooks/2_1_2_Synthetic_Data_Gridding.ipynb
@@ -19,7 +19,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -32,39 +32,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "90b3854760e9410386cafb0d8e25a8ea",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/html": [
-       "<p>Failed to display Jupyter Widget of type <code>interactive</code>.</p>\n",
-       "<p>\n",
-       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
-       "  that the widgets JavaScript is still loading. If this message persists, it\n",
-       "  likely means that the widgets JavaScript library is either not installed or\n",
-       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
-       "  Widgets Documentation</a> for setup instructions.\n",
-       "</p>\n",
-       "<p>\n",
-       "  If you're reading this message in another frontend (for example, a static\n",
-       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
-       "  it may mean that your frontend doesn't currently support widgets.\n",
-       "</p>\n"
-      ],
-      "text/plain": [
-       "interactive(children=(FloatText(value=25.0, description='Grid (m):'), Dropdown(description='Method', index=3, options=('nearest', 'linear', 'cubic', 'minimumCurvature'), value='minimumCurvature'), Dropdown(description='ColorMap', index=3, options=('viridis', 'plasma', 'magma', 'RdBu_r', 'Greys_r', 'jet', 'rainbow', 'pink', 'bone', 'hsv', 'nipy_spectral'), value='RdBu_r'), FloatText(value=nan, description='EPSG code:', disabled=True), ToggleButton(value=False, description='Fetch Inc/Dec', disabled=True, icon='check', tooltip='Connect to NOAA API'), Text(value='./Output/DataGrid', description='GeoTiff name:', disabled=True), ToggleButton(value=False, description='Export Grid', disabled=True, icon='check', tooltip='Write file'), Output()), _dom_classes=('widget-interact',))"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "view = Simulator.dataGriddingWidget(\n",
     "    survey, saveAs=\"./Output/DataGrid\",\n",

diff --git a/Notebooks/2_1_3_Synthetic_Mag_Data_Visualization.ipynb b/Notebooks/2_1_3_Synthetic_Mag_Data_Visualization.ipynb
@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -39,39 +39,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e66616fe777b44de8f363cc4ac3f2ea4",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/html": [
-       "<p>Failed to display Jupyter Widget of type <code>HBox</code>.</p>\n",
-       "<p>\n",
-       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
-       "  that the widgets JavaScript is still loading. If this message persists, it\n",
-       "  likely means that the widgets JavaScript library is either not installed or\n",
-       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
-       "  Widgets Documentation</a> for setup instructions.\n",
-       "</p>\n",
-       "<p>\n",
-       "  If you're reading this message in another frontend (for example, a static\n",
-       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
-       "  it may mean that your frontend doesn't currently support widgets.\n",
-       "</p>\n"
-      ],
-      "text/plain": [
-       "HBox(children=(VBox(children=(FloatSlider(value=270.0, continuous_update=False, description='SunAzimuth', max=360.0, step=5.0), FloatSlider(value=15.0, continuous_update=False, description='SunAngle', max=90.0, step=5.0), FloatSlider(value=0.9, continuous_update=False, description='ColorTransp', max=1.0, step=0.05), FloatSlider(value=0.5, continuous_update=False, description='HSTransp', max=1.0, step=0.05), FloatSlider(value=5.0, continuous_update=False, description='vScale', max=10.0, min=1.0, step=1.0), IntSlider(value=0, continuous_update=False, description='Contours', step=2), Dropdown(description='ColorMap', index=3, options=('viridis', 'plasma', 'magma', 'RdBu_r', 'Greys_r', 'jet', 'rainbow', 'pink', 'bone', 'hsv', 'nipy_spectral'), value='RdBu_r'), FloatRangeSlider(value=(-317.2247314453125, 917.1829223632812), continuous_update=False, description='Color Range', max=917.1829223632812, min=-317.2247314453125, readout_format='.1f', step=1.0), Dropdown(description='Color Normalization', index=1, options=('Linear', 'HistEqualized'), value='HistEqualized')), layout=Layout(height='600px', margin='60px 0px 0px 0px', width='35%')), Output()))"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "view = Simulator.dataHillsideWidget(dataGrid, saveAs='DataHillshade', dpi=300, omit=['EPSGcode','saveAs','SaveGeoTiff'])\n",
     "display(view)"

diff --git a/Notebooks/2_1_4_Synthetic_Mag_Data_Filters.ipynb b/Notebooks/2_1_4_Synthetic_Mag_Data_Filters.ipynb
@@ -23,7 +23,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -34,39 +34,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d6496470d87c4ff196949203f18287f5",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/html": [
-       "<p>Failed to display Jupyter Widget of type <code>HBox</code>.</p>\n",
-       "<p>\n",
-       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
-       "  that the widgets JavaScript is still loading. If this message persists, it\n",
-       "  likely means that the widgets JavaScript library is either not installed or\n",
-       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
-       "  Widgets Documentation</a> for setup instructions.\n",
-       "</p>\n",
-       "<p>\n",
-       "  If you're reading this message in another frontend (for example, a static\n",
-       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
-       "  it may mean that your frontend doesn't currently support widgets.\n",
-       "</p>\n"
-      ],
-      "text/plain": [
-       "HBox(children=(VBox(children=(FloatSlider(value=270.0, continuous_update=False, description='SunAzimuth', max=360.0, step=5.0), FloatSlider(value=15.0, continuous_update=False, description='SunAngle', max=90.0, step=5.0), FloatSlider(value=0.9, continuous_update=False, description='ColorTransp', max=1.0, step=0.05), FloatSlider(value=0.0, continuous_update=False, description='HSTransp', max=1.0, step=0.05), FloatSlider(value=5.0, continuous_update=False, description='vScale', max=10.0, min=1.0, step=1.0), IntSlider(value=0, continuous_update=False, description='Contours', step=2), Dropdown(description='ColorMap', index=3, options=('viridis', 'plasma', 'magma', 'RdBu_r', 'Greys_r', 'jet', 'rainbow', 'pink', 'bone', 'hsv', 'nipy_spectral'), value='RdBu_r'), Dropdown(description='Grid Filters', index=1, options=('TMI', 'derivativeX', 'derivativeY', 'firstVertical', 'totalHorizontal', 'tiltAngle', 'analyticSignal'), value='derivativeX'), FloatSlider(value=0.0, continuous_update=False, description='UpC Height', max=200.0, step=10.0)), layout=Layout(height='600px', margin='60px 0px 0px 0px', width='35%')), Output()))"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "selection = Simulator.gridFiltersWidget(\n",
     "    dataGrid, HSTransp=0, \n",

diff --git a/Notebooks/2_1_5_Synthetic_Mag_Data_DepthSource.ipynb b/Notebooks/2_1_5_Synthetic_Mag_Data_DepthSource.ipynb
@@ -30,7 +30,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,39 +41,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "fac89f97a102407cbfb2de80a1438913",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/html": [
-       "<p>Failed to display Jupyter Widget of type <code>HBox</code>.</p>\n",
-       "<p>\n",
-       "  If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
-       "  that the widgets JavaScript is still loading. If this message persists, it\n",
-       "  likely means that the widgets JavaScript library is either not installed or\n",
-       "  not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
-       "  Widgets Documentation</a> for setup instructions.\n",
-       "</p>\n",
-       "<p>\n",
-       "  If you're reading this message in another frontend (for example, a static\n",
-       "  rendering on GitHub or <a href=\"https://nbviewer.jupyter.org/\">NBViewer</a>),\n",
-       "  it may mean that your frontend doesn't currently support widgets.\n",
-       "</p>\n"
-      ],
-      "text/plain": [
-       "HBox(children=(VBox(children=(FloatSlider(value=270.0, continuous_update=False, description='SunAzimuth', max=360.0, step=5.0), FloatSlider(value=15.0, continuous_update=False, description='SunAngle', max=90.0, step=5.0), FloatSlider(value=0.9, continuous_update=False, description='ColorTransp', max=1.0, step=0.05), FloatSlider(value=0.0, continuous_update=False, description='HSTransp', max=1.0, step=0.05), FloatSlider(value=5.0, continuous_update=False, description='vScale', max=10.0, min=1.0, step=1.0), Dropdown(description='ColorMap', index=4, options=('viridis', 'plasma', 'magma', 'RdBu_r', 'Greys_r', 'jet', 'rainbow', 'pink', 'bone', 'hsv', 'nipy_spectral'), value='Greys_r'), Dropdown(description='Grid Filters', index=1, options=('TMI', 'tiltAngle'), value='tiltAngle'), FloatSlider(value=0.0, continuous_update=False, description='UpC Height', max=200.0, step=10.0), Dropdown(description='Depth Color', options=('viridis', 'plasma', 'magma', 'RdBu_r', 'Greys_r', 'jet', 'rainbow', 'pink', 'bone', 'hsv', 'nipy_spectral'), value='viridis'), FloatSlider(value=1.0, continuous_update=False, description='Marker Size', max=10.0, min=0.1)), layout=Layout(height='600px', margin='60px 0px 0px 0px', width='35%')), Output()))"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "view = Simulator.gridTilt2Depth(dataGrid, HSTransp=0, ColorMap='Greys_r', shapeFile='./assets/Synthetic/Synthetic_Zcontours.shp', omit=['GridFileName', \"EPSGcode\", 'SaveGrid', 'ShapeFileName', 'SaveShape'])\n",
     "display(view)"