Metadata-Version: 1.1
Name: pdsspect
Version: 0.1.0
Summary: PDS Image Viewer
Home-page: https://github.com/planetarypy/pdsspect
Author: PlanetaryPy Developers
Author-email: contact@planetarypy.com
License: BSD
Description: ===============================================================
        pdsspect - A Python PDS Image Region of Interest Selection Tool
        ===============================================================
        
        **NOTE:** This is Alpha quality software that is being actively developed, use
        at your own risk.  This software is not produced by NASA.
        
        * Free software: BSD license
        * Documentation: https://pdsspect.readthedocs.org.
        
        Features
        --------
        
        * NASA PDS Image Viewer
        
        **NOTE:** This is alpha quality software.  It lacks many features and lacks
        support for many PDS image types.  This software is not produced by NASA.
        
        Install
        -------
        
        On OS X you must first install the Qt UI toolkit using Homebrew
        (http://brew.sh/).  After installing Homebrew, issue the following command::
        
            brew install qt
        
        Install Using Pip
        +++++++++++++++++
        Install pdsspect using pip::
          
          pip install pdsspect
        
        Then install your choice of pyside, pyqt4, or pyqt5
        
        Install for Development
        +++++++++++++++++++++++
        
        Create a new virtual environment, install the `pdsspect` module with git,
        and setup the PySide environment. You must install either PySide, PyQt5, or
        PyQt4 as well (recommend PyQt5)::
        
            Make a clone of ``pdsspect`` and change to main directory. We recommend
            making a virtual environment for to install ``pdsspect`` in.
        
            pip install -e .
            pip install PyQt5
        
        Now you should be able to run the `pdsspect` program.
        
        This works on Linux as well (Ubuntu 14.04).  Instructions coming soon.
        
        Quick Tutorial
        --------------
        
        Open an image in the command line::
            
            pdsspect tests/mission_data/2m132591087cfd1800p2977m2f1.img
        
        This will open the default window:
        
        .. image:: screenshots/default1.png
        .. image:: screenshots/default2.png
        .. image:: screenshots/default3.png
        
        The bottom left window is considered the main window. In this window, the user
        can adjust the position of the pan and open other windows. The bottom right
        window is the ``basic`` window. Pressing the ``basic`` button will open this
        window if closed. However, it starts out open. In this window, the user can
        change the image in the views and adjust the cut levels by either moving the
        red lines or typing in the numbers in the cut boxes:
        
        .. image:: screenshots/set_cuts1.png
        .. image:: screenshots/set_cuts2.png
        
        The top window is the ``pan window`` which displays the data in the main
        window's red box. The main function of this window is to make Region of
        Interest (ROI) selections.
        
        In the ``zoom`` box in the main window, the user can change the size of the box
        and the data in the pan view:
        
        .. image:: screenshots/zoom1.png
        .. image:: screenshots/zoom2.png
        
        the mouse wheel can also be used to change the zoom. Rolling the wheel foward
        and backwards will adjust the zoom amount by ``+1`` or ``-1`` respectively.
        The user can adjust the position of the box by clicking in the main window
        where the center of the pan should be. Using the arrow keys will also adjust
        the position of the box by ``1`` in the direction of the arrow key.
        
        Clicking the ``Add Window`` button will open another view. This view will have
        the same image, cut levels, and zoom by default.
        
        .. image:: screenshots/multiple_window1.png
        
        If the image's are the same, chaning the cut levels on one image will
        automatically change the cut levels on another image. However, one can change
        the zoom on one view without changing the zoom another view.
        
        .. image:: screenshots/multiple_window2.png
        .. image:: screenshots/multiple_window3.png
        .. image:: screenshots/multiple_window4.png
        
        When the images are different, adjusting the cut levels on one image will only
        change the cut levels on that image:
        
        .. image:: screenshots/different_cuts1.png
        .. image:: screenshots/different_cuts2.png
        
        The user can create separate ROIs in each view:
        
        .. image:: screenshots/roi1.png
        
        Clicking the ``Selection`` button will open the ``Selections Window``:
        
        .. image:: screenshots/selection1.png
        
        In this window, the user can choose the color of the ROI. The possible choices
        for colors: ``red``, ``brown``, ``lightblue``, ``lightcyan``, ``darkgreen``,
        ``yellow``, ``pink``, ``teal``, ``goldenrod``, ``sienna``, ``darkblue``,
        ``crimson``, ``maroon``, ``purple``, and ``eraser (black)``. The selection type
        can be changed in this window as well. The possible types are ``filled
        rectangle``, ``filled polygon``, and ``pencil`` (single points).
        
        Furthermore, in this window, the user can clear the current color or clear all
        ROIs. Most importantly, the user can export ROIs to ``.npz`` files. These files
        contain boolean masks and of the images and a list of files open at the time
        of export. The ROIs in the 2nd, 3rd, 4th, etc. views will be labeled as 
        ``color#view`` while the ROIs in the first view is still labeled as ``color``.
        For example, to see the data in an example file ``example.npz``, use `numpy
        load method
        <https://docs.scipy.org/doc/numpy-1.13.0/reference/generated/numpy.load.html>`_
        to view and utilize data.
        
        .. code-block:: python
        
            >>> import numpy as np
            >>> selections = np.load('example.npz')
            >>> selections['red'][114:118, 142:146]
            array([[ True,  True,  True,  True],
                   [ True,  True,  True,  True],
                   [ True,  True,  True,  True],
                   [ True,  True,  True,  True]], dtype=bool)
            >>> selections['purple2'][48:52, 146:150]
            array([[False, False, False, False],
                   [False,  True,  True,  True],
                   [ True,  True,  True,  True],
                   [ True,  True,  True,  True]], dtype=bool)
        
        The user can also import ROI selections. However the images that are open must
        be in the ``files`` list in the ``.npz`` file.
        
        Changing the opacity in the Selecitons window will change the opacity on all
        the ROIs in every view:
        
        .. image:: screenshots/opacity1.png
        .. image:: screenshots/opacity2.png
        
        
        You can view the data within the ROIs with the ``ROI Histogram`` window. Open
        the window by pressing the ``ROI Histogram`` button in the main viewer.
        
        .. image:: screenshots/histogram1.png
        
        Display the data in the ROI by color by checking the checkbox next to the
        color. When the image in the menu and the current image in the checked view are
        the same, the plot will be a histogram:
        
        .. image:: screenshots/histogram2.png
        
        When the menu and the current image are different, the plot will compare the
        data:
        
        .. image:: screenshots/histogram3.png
        
        To view the data in the other view, check the view number:
        
        .. image:: screenshots/histogram4.png
        
        Overlay ROIs by checking other boxes. The order (depth) of the histogram data
        will be in the order that the user checks the boxes (i.e., checking red and
        then purple will result in purple overlaying the red).
        
        To perform multispectral analysis use ``ROI Line Plot``.
        If analyzing images that are not :ref:`fully supported (see here for list of
        instruments supported by pdsspect) <supported-instruments>` the user must
        manually input the image wavelength with ``Set Wavelength`` widget:
        
        .. image:: screenshots/set_wavelength1.png
        
        ``ROI Line Plot`` works similar to that of the histogram plot except it will
        compare each image with an associated wavelength.
        
        .. image:: screenshots/line_plot1.png
        .. image:: screenshots/line_plot2.png
        .. image:: screenshots/line_plot3.png
        
        The user can flip the image over different axis with the Transforms window.
        The transformation will apply to each image in all the views:
        
        .. image:: screenshots/transforms1.png
        .. image:: screenshots/transforms2.png
        .. image:: screenshots/transforms3.png
        
        Note that when opening multiple images at the same time, it is best practice
        that they are all the same shape. Otherwise the images will have the smallest
        common shape and not look as expected (i.e., If when loading two images where
        one image has a shape of ``(63, 36)`` and the other image has a shape of
        ``(24, 42)``, the displayed shape will be ``(24, 36)``. This will cause the
        first image to have the right side cut off and the second image to have the
        top cut off). This is done so all ROIs created can apply to the entire list
        of images. To avoid this behavior, either only open images that have the same
        shape or open images one at a time.
        
        
        Images In Example
        +++++++++++++++++
        
        * `2p235913308radau37p2111l2c1.img 
          <http://pds-geosciences.wustl.edu/mer/mer2-m-pancam-3-radcal-rdr-v1/
          mer2pc_1xxx/data/sol1234/2p235913308radau37p2111l2c1.img>`_
        * `2p235913328radau37p2111l3c1.img
          <http://pds-geosciences.wustl.edu/mer/mer2-m-pancam-3-radcal-rdr-v1/
          mer2pc_1xxx/data/sol1234/2p235913328radau37p2111l3c1.img>`_
        * `2p235913348radau37p2111l4c1.img
          <http://pds-geosciences.wustl.edu/mer/mer2-m-pancam-3-radcal-rdr-v1/
          mer2pc_1xxx/data/sol1234/2p235913348radau37p2111l4c1.img>`_
        * `2p235913368radau37p2111l5c1.img
          <http://pds-geosciences.wustl.edu/mer/mer2-m-pancam-3-radcal-rdr-v1/
          mer2pc_1xxx/data/sol1234/2p235913368radau37p2111l5c1.img>`_
        * `2p235913399radau37p2111l6c1.img
          <http://pds-geosciences.wustl.edu/mer/mer2-m-pancam-3-radcal-rdr-v1/
          mer2pc_1xxx/data/sol1234/2p235913399radau37p2111l6c1.img>`_
        * `2p235913431radau37p2111l7c1.img
          <http://pds-geosciences.wustl.edu/mer/mer2-m-pancam-3-radcal-rdr-v1/
          mer2pc_1xxx/data/sol1234/2p235913431radau37p2111l7c1.img>`_
        
        .. _supported-instruments:
        
        Supported Instruments
        +++++++++++++++++++++
        
        .. include:: supported_instruments.rst
        
        Adding More Instruments
        ~~~~~~~~~~~~~~~~~~~~~~~
        
        We welcome anyone to create more models for instruments that are not yet
        supported. Please follow the Pull Request guide to make sure your model is
        compatible with the rest of the models. See `Pull Request #20
        <https://github.com/planetarypy/pdsspect/pull/20>`_ as an example.
        
        Pull Request Checklist
        ######################
        
        Please include the following checklist in your PR so we know you have completed
        each step::
        
          - [ ] Created model as subclass of [InstrumentBase](https://github.com/planetarypy/pdsspect/blob/master/instrument_models/instrument.py#L7)
          - [ ] Added model to [get_wavelength](https://github.com/planetarypy/pdsspect/blob/master/instrument_models/get_wavelength.py)
          - [ ] Documented Model
          - [ ] Tested Model
          - [ ] Added model to [test_get_wavelength](https://github.com/planetarypy/pdsspect/blob/master/tests/test_get_wavelength.py) test
          - [ ] Added instrument to supported_instruments.rst list
        
        
        Style
        #####
        
        * Set PR label to ``Instrument Model``
        * If an issue was created, please include ``Fixes #<issue_number>`` at the top
          of the PR to automatically close the issue
        * Please include a link to any documents used to find the filter wavelength.
          Follow the example for `Mastcam
          <https://github.com/planetarypy/pdsspect/blob/master/instrument_models/
          mastcam.py>`_
          and/or `Pancam
          <https://github.com/planetarypy/pdsspect/blob/master/instrument_models/
          pancam.py>`_
        * When documenting your model, use `numpy docs
          <https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`_.See
          these `examples <http://sphinxcontrib-napoleon.readthedocs.io/en/latest/
          example_numpy.html>`_. Also add to `instrument_models.rst
          <https://github.com/planetarypy/pdsspect/blob/master/docs/
          instrument_models.rst>`_ following the format of the other models
        * For tests, if one of the core mission_data images is not from your instrument,
          create a minimal label in the `tests\\__init__.py
          <https://github.com/planetarypy/pdsspect/blob/master/tests/__init__.py>`_.
          You must test the model itself and test that it works in
          `test_get_wavelength <https://github.com/planetarypy/pdsspect/blob/master/
          tests/test_get_wavelength.py>`_
        * Add the mission and instrument to the ``supported_instruments.rst`` file
          following the set format.
        
        
        
        
        
        
        History
        -------
        
        0.1.0 ("2017-08-20")
        --------------------
        
        * First release on PyPi
        
Keywords: pdsspect
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
