added quality reports to notebooks, updated instal docs

AndrewAnnex · May 30, 2021 · 3095c28 · 3095c28
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diff --git a/asap_stereo/asap_ctx_workflow.ipynb b/asap_stereo/asap_ctx_workflow.ipynb
@@ -168,6 +168,33 @@
     }
    }
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Stereo Quality Report"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "qual_report = asap.CommonSteps().get_stereo_quality_report(f'{left}_{right}/{left}.lev1eo.cub', f'{left}_{right}/{right}.lev1eo.cub')\n",
+    "print(qual_report)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
   {
    "cell_type": "markdown",
    "source": [

diff --git a/asap_stereo/asap_hirise_workflow.ipynb b/asap_stereo/asap_hirise_workflow.ipynb
@@ -60,7 +60,8 @@
    "outputs": [],
    "source": [
     "from IPython.display import Image\n",
-    "from asap_stereo import asap"
+    "from asap_stereo import asap\n",
+    "import math"
    ]
   },
   {
@@ -179,6 +180,30 @@
     "!asap hirise step-four "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Stereo Quality Report"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "qual_report = asap.CommonSteps().get_stereo_quality_report(f'{left}_{right}/{left}.mos_hijitreged.norm.cub', f'{left}_{right}/{right}.mos_hijitreged.norm.cub')\n",
+    "print(qual_report)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
   {
    "cell_type": "markdown",
    "source": [
@@ -201,7 +226,7 @@
     "    # this is because rescale in ISIS does not update GSD in metadata\n",
     "    asap.CommonSteps().rescale_and_overwrite(factor=downsample, postfix='.mos_hijitreged.norm.cub')\n",
     "    img_gsd = math.ceil(res_gsd)*downsample\n",
-    "    dem_gsd = 4*imggsd\n",
+    "    dem_gsd = 4*img_gsd\n",
     "    print('new img gsd', img_gsd)\n",
     "    print('new dem gsd', dem_gsd)\n"
    ],

diff --git a/docs/install.rst b/docs/install.rst
@@ -2,58 +2,65 @@
 Installation
 ============
 
-This guide assumes that the user has already installed anaconda.
+This guide assumes that the user has already installed anaconda with conda version newer than 4.9.
+
+ASAP requires that Install both Ames Stereo Pipeline and ISIS are available to the user in the PATH, and the user will need to have downloaded the relevant ISIS data folders.
+Below we provide a guide assuming the user has a working ISIS installation in some other conda environment, and a a local copy of the pre-compiled Ames Stereo Pipeline.
+Please refer to the `Ames Stereo Pipeline Installation <https://stereopipeline.readthedocs.io/en/latest/installation.html#precompiled-binaries-linux-and-macos>`_ documentation for details on how to download the precompiled ASP.
+
+We will create a new conda environment for ASAP that includes the bin directories in the PATH for ASAP and the ISIS data folder environment variables.
+In the variables section, you will need to update the parameters for your environment.
+The ISISROOT directory is the conda environment folder for your working ISIS installation, for example "~/anaconda/envs/isis/", it can also be found by activating the environment and printing the $CONDA_PREFIX variable.
+The two ISIS data directories are explained in the `ISIS installation documentation <https://github.com/USGS-Astrogeology/ISIS3>`_.
+The ASPROOT directory similarly points to the unzipped archive of the Ames Stereo Pipeline.
 
-ASAP requires that Install both Ames Stereo Pipeline and ISIS are available to the user in the PATH.
-There are several ways to do this outside of this guide's scope, but a simple solution is to use the 
-following conda environment YAML configuration file:
 
 .. code-block:: yaml
 
-   name: asap_0_0_4
+   name: asap_0_2_0
    channels:
-     - nasa-ames-stereo-pipeline
-     - usgs-astrogeology
      - conda-forge
      - defaults
    dependencies:
-     - python=3.6
-     - stereo-pipeline==2.7.0
+     - python=3.8
      - nb_conda_kernels
      - jupyterlab
      - requests
      - fire
      - tqdm
      - sh
      - papermill
+     - rasterio
+     - pyproj
+     - shapely
+     - pvl
      - pip 
      - pip:
-       - rasterio
-       - pyproj
        - moody>=0.0.4
-       - asap_stereo>=0.0.4 
+       - asap_stereo=0.2.0
+   variables:
+     ISISROOT: /path/to/your/isis/conda/env/
+     ISISDATA: /path/to/your/isis/data/dir/
+     ISISTESTDATA: /path/to/optional/isis/test/data/dir/
+     ASPROOT: /path/to/your/precompiled/StereoToolkitDirectory/
 
 
 Using the command::
 
-    conda env create  --file asaptest.yml
-
-Will create a new conda environment called "asap_0_0_4". 
-At this point, ASAP will be available to the user.
-However, the user must download the `ISIS Data Area  <https://github.com/USGS-Astrogeology/ISIS3#the-isis-data-area>`_ 
-and run the `ISIS variable initialization script <https://github.com/USGS-Astrogeology/ISIS3#isis-installation-with-conda>`_
-to finish the installation. Steps for these last two steps are available in the ISIS README and documentation linked to before. 
-Be sure to run the variable initialization script in your new conda environment by first running:: 
-
-    conda activate asap_0_0_4
+    conda env create --file asap.yml
 
-and then::
+This will create a new conda environment called "asap_0_2_0". The environment however is not ready to use yet.
+We need to update the path to ensure ASP and ISIS programs are available for ASAP to use.
+To do this run the following commands::
 
-    python $CONDA_PREFIX/scripts/isis3VarInit.py <any args...>
+    conda activate asap_0_2_0
+    conda env config vars set PATH=$PATH:$ASPROOT/bin:$ISISROOT/bin
+    conda deactivate
 
-Deactivate, then reactivate the environment, and you are ready to start using asap! 
+This will update the PATH variable in the conda environment to include both ISIS and ASP bin folders.
+At this point you are ready to start using asap!
 
-To test if asap is installed correctly, run each of the following::
+To test if asap is installed correctly, run each of the following after activating the new environment::
 
     asap
     asap ctx