Welcome to pdsspect’s documentation!¶

pdsspect - A Python PDS Image Region of Interest Selection Tool¶

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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).

Quick Tutorial¶

Open an image in the command line:

pdsspect tests/mission_data/2m132591087cfd1800p2977m2f1.img

This will open the default window:

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:

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:

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.

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.

When the images are different, adjusting the cut levels on one image will only change the cut levels on that image:

The user can create separate ROIs in each view:

Clicking the Selection button will open the Selections Window:

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 to view and utilize data.

>>> 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:

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.

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:

When the menu and the current image are different, the plot will compare the data:

To view the data in the other view, check the view number:

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 fully supported (see here for list of instruments supported by pdsspect) the user must manually input the image wavelength with Set Wavelength widget:

ROI Line Plot works similar to that of the histogram plot except it will compare each image with an associated wavelength.

The user can flip the image over different axis with the Transforms window. The transformation will apply to each image in all the views:

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¶

Supported Instruments¶

MER
- Pancam
MSL
- Mastcam
Cassini
- Imaging Science Subsystem (ISS)

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 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 and/or Pancam
When documenting your model, use numpy docs.See these examples. Also add to 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. You must test the model itself and test that it works in test_get_wavelength
Add the mission and instrument to the supported_instruments.rst file following the set format.

pdsspect¶

class pdsspect.pdsspect.PDSSpect(image_set)[source]¶

Bases: PyQt5.QtWidgets.QMainWindow, pdsspect.pdsspect_image_set.PDSSpectImageSetViewBase

Main Window of pdsspect

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model

image_set¶: PDSSpectImageSet – The model for each view

pdsspect_view¶: PDSSpectViewWidget – The main viewer for panning

pan_view¶: PanView – The view in which the user makes ROI selections

selection_btn¶: QtWidgets.QPushButton – Button to open the selections window

selection_window¶: Selection – The selection window to adjust ROI, import ROIs, and export ROIs

basic_btn¶: QtWidgets.QPushButton – Button to open the basic window

basic_window¶: BasicWidget – Window to adjust cut levels and change images

transforms_btn¶: QtWidgets.QPushButton – Open Transforms window

transforms_window¶: Transforms – Window to flip x axis, flip y axis, or switch x and y axis

roi_histogram_btn¶: QPushButton – Open ROI Histogram window

roi_histogram_window¶: ROIHistogramWidget – The ROI Histogram Window

roi_line_plot_btn¶: QPushButton – Open ROI Line Plot window

roi_line_plot_window¶: ROILinePlotWidget – The ROI Line Plot Window

add_window_btn¶: QPushButton – Add another window

quit_btn¶: QtWidgets.QPushButton – Quit

button_layout1¶: QtWidgets.QHBoxLayout – Layout for the buttons. If you want to re-adjust where the buttons go, override this attribute

button_layout2¶: QtWidgets.QHBoxLayout – Layout for the buttons. If you want to re-adjust where the buttons go, override this attribute

main_layout¶: QtWidgets.QVBoxLayout – Place the image viewer over the buttons. Overide this attribute if changing overall layout

add_window()[source]¶: Add another window to make more ROIs

image_sets¶: list – All the image sets, including the current one

open_basic()[source]¶: Open the Basic Window

open_roi_histogram()[source]¶: Open the ROI Histogram Window

open_roi_line_plot()[source]¶: Open the ROI Line Plot Window

open_selection()[source]¶: Open the Selection Window

open_set_wavelengths()[source]¶: Open Set Wavelengths window

open_transforms()[source]¶: Open the Transforms Window

quit(*args)[source]¶: Quit pdsspect

pdsspect.pdsspect.pdsspect(inlist=None)[source]¶

Run pdsspect from python shell or command line with arguments

Parameters:	inlist (`list`) – A list of file names/paths to display in the pdsspect

Examples

From the command line:

To view all images from current directory

pdsspect

To view all images in a different directory

pdsspect path/to/different/directory/

This is the same as:

pdsspect path/to/different/directory/*

To view a specific image or types of images

pdsspect 1p*img

To view images from multiple directories:

pdsspect * path/to/other/directory/

From the (i)python command line:

>>> from pdsspect.pdsspect import pdsspect
>>> pdsspect()
Displays all of the images from current directory
>>> pdsspect('path/to/different/directory')
Displays all of the images in the different directory
>>> pdsspect ('1p*img')
Displays all of the images that follow the glob pattern
>>> pdsspect('a1.img, b*.img, example/path/x*img')
You can display multiple images, globs, and paths in one window by
separating each item by a command
>>> pdsspect(['a1.img, b3.img, c1.img, d*img'])
You can also pass in a list of files/globs
pdsspect returns a dictionary of the ROIs:
>>> rois = pdsspect(['a1.img, b3.img, c1.img, d*img'])
>>> rois['red'][:2, :2]
array(
    [
        [False, False],
        [False, False]
    ],
    dtype=bool
)

pdsspect_image_set¶

The main model for all the views in pdsspect

class pdsspect.pdsspect_image_set.ImageStamp(filepath, metadata=None, logger=None, wavelength=nan, unit='nm')[source]¶

Bases: ginga.BaseImage.BaseImage

BaseImage for the image view canvas

Parameters:

filepath (str) – The path to the image to be opened
metadata (None) – Metadata for BaseImage
logger (None) – logger for BaseImage
wavelength (float [nan]) – Image’s filter wavelength. If nan, will try to use instrument_models.get_wavelength.get_wavelength() to get the wavelength
unit (str [nm]) – Wavelength unit. Must be one of accepted_units

pds_image¶: PDS3Image – Image object that holds data and the image label

image_name¶: str – The basename of the filepath

seen¶: bool – False if the image has not been seen by the viewer. True otherwise Default if False

cuts¶: tuple – The cut levels of the image. Default is two None types

accepted_units¶: list – List of accepted units: nm, um, and AA

data¶: numpy.ndarray – Image data

get_wavelength()[source]¶: astropy.units.quantity.Quantity Copy of the wavelength

unit¶

astropy.units.Unit – The wavelength unit

Setting the unit will convert the wavelength value as well. The new unit must also be one of the accepted_units

wavelength¶: int – The images wavelength

class pdsspect.pdsspect_image_set.PDSSpectImageSet(filepaths)[source]¶

Bases: object

Model for each view is pdsspect

The images loaded should all have 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.

Parameters:	filepaths (`list`) – List of filepaths to images

colors¶

list of str – List of possible color names to make ROIs.

The possible choices for colors: red, brown, lightblue, lightcyan, darkgreen, yellow, pink, teal, goldenrod, sienna, darkblue, crimson, maroon, purple, and eraser (black)

selection_types¶: list of str – Selection types for making ROIs. The possible types are Filled Rectangle, Filled Polygon, and Filled Rectangle, (single points).

accepted_units¶: list – List of accepted units: nm, um, and AA

images¶: list of ImageStamp – Images to view and make selections. Must all have the same dimensions

filepaths¶: list – List of filepaths to images

current_color_index¶: int – Index of the current color in colors list for ROI creation (Default is 0)

add_coords_to_roi_data_with_color(coordinates, color)[source]¶

Add coordinates to ROI data in the with the given color

Parameters:	coordinates (`numpy.ndarray` or `tuple`) – Either a `(m x 2)` array or a tuple of two arrays If an array, the first column are the x coordinates and the second are the y coordinates. If a tuple of arrays, the first array are x coordinates and the second are the corresponding y coordinates. color (`str`) – The name a color in `colors`

add_subset(subset)[source]¶

Add a subset to the list of subsets

Parameters:	subset (`SubPDSSpectImageSet`) – Subset to add to the list of subsets

all_rois_coordinates¶: tuple of two numpy.ndarray – Coordinates of where there is a pixel selected in a ROI

alpha¶

float – The alpha value between 0 and 1

Setting the alpha value will change the opacity of all the ROIs and then set the data in the views

alpha255¶: float The alpha value normalized between 0 and 255

center¶

tuple of two float – x and y coordinate of the center of the pan.

Setting the center will move the pan to the new center. The center points cannot result in the pan being out of the image. If they are they will be changed so the pan only goes to the edge.

color¶: str – The current color in the colors list determined by current_color_index

create_subset()[source]¶

Create a subset and add it to the list of subsets

Returns:	subset – The newly created subset
Return type:	`SubPDSSpectImageSet`

current_image¶: ImageStamp – The current image determined by current_image_index

current_image_index¶

int – Index of the current image in images

Setting the index will set the image in the views

delete_all_rois()[source]¶: Delete all of the ROIs

delete_rois_with_color(color)[source]¶

Delete the ROIs with the given color

Parameters:	color (`str`) – The name a color in `colors`

edges¶: tuple of four float – The left, bottom, right and top edges of the pan

filenames¶: list of str – Basenames of the filepaths

flip_x¶

bool – If True, flip the x axis

Setting the flip_x will display the transformation in the views

flip_y¶

bool – If True, flip the y axis

Setting the flip_y will display the transformation in the views

get_coordinates_of_color(color)[source]¶

The coordinates of the ROI with the given color

Parameters:	color (`str`) – The name a color in `colors`
Returns:	coordinates – The first array are the x coordinates and the second are the corresponding y coordinates
Return type:	`tuple` of two `numpy.ndarray`

map_zoom_to_full_view()[source]¶

Get the change in x and y values to the center of the image

Returns:	delta_x (`float`) – The horizontal distance to the center of the full image delta_y (`float`) – The vertical distance to the center of the full image

pan_data¶: numpy.ndarray – The data within the pan

pan_height¶: float – Height of the pan area

pan_roi_data¶: numpy.ndarray – The ROI data in the pan

pan_slice¶: numpy.s_ – Slice of pan to extract data from an array

pan_width¶: float – Width of the pan area

register(view)[source]¶: Register a View with the model

remove_subset(subset)[source]¶

Remove a subset to the list of subsets

Parameters:	subset (`SubPDSSpectImageSet`) – Subset to remove to the list of subsets

reset_center()[source]¶: Reset the pan to the center of the image

selection_index¶: int – Index of the ROI selection type

selection_type¶: str – The current selection type in selection_types determined by selection_index

set_unit()[source]¶: Set each image to unit

simultaneous_roi¶

bool – If true, new ROIs appear in every view

Setting simultaneous_roi will set all windows to have the same ROIs as the first window. Any new ROI created will appear in each window

subsets¶: list of SubPDSSpectImageSet – The list of subsets

swap_xy¶

bool – If True, swap the x and y axis

Setting the swap_xy will display the transformation in the views

transforms¶: tuple of bool – the flip_x, flip_y, and swap_xy transformations

unit¶: str – The image set’s current wavelength unit

unregister(view)[source]¶: Unregister a View with the model

x_radius¶: float – Half the image width

y_radius¶: float – Half the image height

zoom¶

int – Zoom factor for the pan

The zoom factor determines the width and height of the pan area. For example, if zoom=2, then the width would be half the image width and the height would be half the image height. Setting the zoom will adjust the pan size in the views.

class pdsspect.pdsspect_image_set.SubPDSSpectImageSet(parent_set)[source]¶

Bases: pdsspect.pdsspect_image_set.PDSSpectImageSet

A Subset of an PDSSpectImageSet

Parameters:	parent_set (`PDSSpectImageSet`) – The subset’s parent

parent_set¶: PDSSpectImageSet – The subset’s parent

add_coords_to_roi_data_with_color(coordinates, color)¶

Add coordinates to ROI data in the with the given color

Parameters:	coordinates (`numpy.ndarray` or `tuple`) – Either a `(m x 2)` array or a tuple of two arrays If an array, the first column are the x coordinates and the second are the y coordinates. If a tuple of arrays, the first array are x coordinates and the second are the corresponding y coordinates. color (`str`) – The name a color in `colors`

add_subset(subset)¶

Add a subset to the list of subsets

Parameters:	subset (`SubPDSSpectImageSet`) – Subset to add to the list of subsets

all_rois_coordinates¶: tuple of two numpy.ndarray – Coordinates of where there is a pixel selected in a ROI

alpha¶

float – The alpha value between 0 and 1

Setting the alpha value will change the opacity of all the ROIs and then set the data in the views

alpha255¶: float The alpha value normalized between 0 and 255

center¶

tuple of two float – x and y coordinate of the center of the pan.

Setting the center will move the pan to the new center. The center points cannot result in the pan being out of the image. If they are they will be changed so the pan only goes to the edge.

color¶: str – The current color in the colors list determined by current_color_index

create_subset()¶

Create a subset and add it to the list of subsets

Returns:	subset – The newly created subset
Return type:	`SubPDSSpectImageSet`

current_image¶: ImageStamp – The current image determined by current_image_index

current_image_index¶

int – Index of the current image in images

Setting the index will set the image in the views

delete_all_rois()¶: Delete all of the ROIs

delete_rois_with_color(color)¶

Delete the ROIs with the given color

Parameters:	color (`str`) – The name a color in `colors`

edges¶: tuple of four float – The left, bottom, right and top edges of the pan

filenames¶: list of str – Basenames of the filepaths

flip_x¶

bool – If True, flip the x axis

Setting the flip_x will display the transformation in the views

flip_y¶

bool – If True, flip the y axis

Setting the flip_y will display the transformation in the views

get_coordinates_of_color(color)¶

The coordinates of the ROI with the given color

Parameters:	color (`str`) – The name a color in `colors`
Returns:	coordinates – The first array are the x coordinates and the second are the corresponding y coordinates
Return type:	`tuple` of two `numpy.ndarray`

map_zoom_to_full_view()¶

Get the change in x and y values to the center of the image

Returns:	delta_x (`float`) – The horizontal distance to the center of the full image delta_y (`float`) – The vertical distance to the center of the full image

pan_data¶: numpy.ndarray – The data within the pan

pan_height¶: float – Height of the pan area

pan_roi_data¶: numpy.ndarray – The ROI data in the pan

pan_slice¶: numpy.s_ – Slice of pan to extract data from an array

pan_width¶: float – Width of the pan area

register(view)¶: Register a View with the model

remove_subset(subset)¶

Remove a subset to the list of subsets

Parameters:	subset (`SubPDSSpectImageSet`) – Subset to remove to the list of subsets

reset_center()¶: Reset the pan to the center of the image

selection_index¶: int – Index of the ROI selection type

selection_type¶: str – The current selection type in selection_types determined by selection_index

set_unit()¶: Set each image to unit

simultaneous_roi¶

bool – If true, new ROIs appear in every view

Setting simultaneous_roi will set all windows to have the same ROIs as the first window. Any new ROI created will appear in each window

subsets¶: list of SubPDSSpectImageSet – The list of subsets

swap_xy¶

bool – If True, swap the x and y axis

Setting the swap_xy will display the transformation in the views

transforms¶: tuple of bool – the flip_x, flip_y, and swap_xy transformations

unit¶: str – The image set’s current wavelength unit

unregister(view)¶: Unregister a View with the model

x_radius¶: float – Half the image width

y_radius¶: float – Half the image height

zoom¶

int – Zoom factor for the pan

The zoom factor determines the width and height of the pan area. For example, if zoom=2, then the width would be half the image width and the height would be half the image height. Setting the zoom will adjust the pan size in the views.

pdsspect_view¶

Window to pan the main image and open other dialog windows

class pdsspect.pdsspect_view.PDSSpectViewController(model, view)[source]¶

Bases: object

Controller for the PDSSpectView

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model view (`PDSpectView`) – View to control

change_pan_center(x, y)[source]¶

Change the center of the pan

Parameters:	x (`float`) – The x coordinate of the center of the pan y (`float`) – The y coordinate of the center of the pan

change_pan_size(zoom)[source]¶

Change the size of the pan by changing the zoom factor

Parameters:	zoom (`float`) – The new zoom factor

class pdsspect.pdsspect_view.PDSSpectView(image_set)[source]¶

Bases: PyQt5.QtWidgets.QWidget, pdsspect.pdsspect_image_set.PDSSpectImageSetViewBase

View to pan the main image

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model

image_set¶: PDSSpectImageSet – pdsspect model

controller¶: PDSSpectViewController

main_layout¶: QtWidgets.QVBoxLayout

zoom_layout¶: QtWidgets.QHBoxLayout – Layout for zoom_label and zoom_text

zoom_label¶: QtWidgets.QLabel – Label the zoom_text text box

zoom_text¶: QtWidgets.QLineEdit – Text box to enter the zoom factor. Zoom will change on return key

view_canvas¶: PDSImageViewCanvas – canvas to place the image on

pan¶: ginga.canvas.types.basic.Box – Pan that represents the pan. Data inside the pan is displayed in PanView

pan_view¶: PanView – View to display data in the pan

adjust_pan_size()[source]¶: Change the pan size as deterined by image_set

arrow_key_move_center(view_canvas, keyname)[source]¶

Adjust center with arrow press by a single pixel

Parameters:	view_canvas (`view_canvas`) – The view canvas keyname (`str`) – Name of the key

change_center(view_canvas, button, data_x, data_y)[source]¶

Adjust center to mouse position. Arguments supplied by callback

Parameters:	view_canvas (`view_canvas`) – The view canvas button (`qtpy.QtCore.QMouseButton`) – The mouse button pressed data_x (`float`) – x coordinate of mouse data_y (`float`) – y coordinate of the mouse

change_zoom()[source]¶: Change zoom to what is in the text box

move_pan()[source]¶: Move the pan as determined by the image_set

redraw()[source]¶: Redraw the view_canvas

set_image()[source]¶: Set image on view_canvas

set_transforms()[source]¶: Apply transforms flip_x, flip_y, and switch_xy

zoom_with_scroll(view_canvas, zoom_event)[source]¶

Change the zoom by 1 with the mouse wheel

Parameters:	view_canvas (`view_canvas`) – The view canvas zoom_event (`ginga.Bindings.ScrollEvent`) – The zoom event

class pdsspect.pdsspect_view.PDSSpectViewWidget(image_set)[source]¶

Bases: PyQt5.QtWidgets.QWidget

Widget to hold the the differen PDSSpectView

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model

image_set¶: PDSSpectImageSet – pdsspect model

create_spect_view(image_set)[source]¶

Create a PDSSpectView and add to the widget

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model
Returns:	spect_view – `PDSSpectView` added to the widget
Return type:	`PDSSpectView`

pan_view¶

Display data in pan and make ROI selections

class pdsspect.pan_view.PanViewController(image_set, view)[source]¶

Bases: object

Controller for the PanView

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model view (`PanView`) – View to control

image_set¶: PDSSpectImageSet – pdsspect model

view¶: PanView – View to control

add_ROI(coordinates)[source]¶

Add a region of interest

Parameters:

coordinates (numpy.ndarray or tuple) –

Either a (m x 2) array or a tuple of two arrays

If an array, the first column are the x coordinates and the second are the y coordinates. If a tuple of arrays, the first array are x coordinates and the second are the corresponding y coordinates.

erase_ROI(coordinates)[source]¶

Erase any region of interest inside coordinates

Parameters:

coordinates (numpy.ndarray or tuple) –

Either a (m x 2) array or a tuple of two arrays

If an array, the first column are the x coordinates and the second are the y coordinates. If a tuple of arrays, the first array are x coordinates and the second are the corresponding y coordinates.

class pdsspect.pan_view.PanView(image_set, parent=None)[source]¶

Bases: PyQt5.QtWidgets.QWidget, pdsspect.pdsspect_image_set.PDSSpectImageSetViewBase

View of the image inside the pan

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model parent (None) – The parent of the view

image_set¶: PDSSpectImageSet – pdsspect model

controller¶: PanViewController – The view’s controller

parent¶: None – The view’s parent

main_layout¶: QtWidgets.QVBoxLayout – The main layout of the view

view_canvas¶: PDSImageViewCanvas – Canvas to view the image

check_ROI_in_pan(func)[source]¶: Wrapper to make sure ROI stays inside the current view

check_roi_in_process(func)[source]¶: Wrapper to make sure the roi making is in process

continue_ROI(view_canvas, button, data_x, data_y)[source]¶: Continue the ROI making on click

extend_ROI(view_canvas, button, data_x, data_y)[source]¶: Extend the ROI on mouse motion

is_erasing¶: bool – True if current color is eraser false otherwise

move_pan()[source]¶: Set the data when the pan is moved

redraw()[source]¶: Redraw view_canvas

save_frame()[source]¶: Save current frame as image

set_data()[source]¶: Set pan data on the canvas

set_image()[source]¶: Set the data

set_roi_data()[source]¶: Set the ROI data on the canvas

start_ROI(view_canvas, button, data_x, data_y)[source]¶: Start the ROI at the mouse location

stop_ROI(view_canvas, button, data_x, data_y)[source]¶: Stop ROI on right click

class pdsspect.pan_view.PanView(image_set, parent=None)[source]

Bases: PyQt5.QtWidgets.QWidget, pdsspect.pdsspect_image_set.PDSSpectImageSetViewBase

View of the image inside the pan

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model parent (None) – The parent of the view

image_set: PDSSpectImageSet – pdsspect model

controller: PanViewController – The view’s controller

parent: None – The view’s parent

main_layout: QtWidgets.QVBoxLayout – The main layout of the view

view_canvas: PDSImageViewCanvas – Canvas to view the image

check_ROI_in_pan(func)[source]: Wrapper to make sure ROI stays inside the current view

check_roi_in_process(func)[source]: Wrapper to make sure the roi making is in process

continue_ROI(view_canvas, button, data_x, data_y)[source]: Continue the ROI making on click

extend_ROI(view_canvas, button, data_x, data_y)[source]: Extend the ROI on mouse motion

is_erasing: bool – True if current color is eraser false otherwise

move_pan()[source]: Set the data when the pan is moved

redraw()[source]: Redraw view_canvas

save_frame()[source]: Save current frame as image

set_data()[source]: Set pan data on the canvas

set_image()[source]: Set the data

set_roi_data()[source]: Set the ROI data on the canvas

start_ROI(view_canvas, button, data_x, data_y)[source]: Start the ROI at the mouse location

stop_ROI(view_canvas, button, data_x, data_y)[source]: Stop ROI on right click

pds_image_view_canvas¶

class pdsspect.pds_image_view_canvas.PDSImageViewCanvas[source]¶

Bases: ginga.qtw.ImageViewCanvasQt.ImageViewCanvas

ImageViewCanvas for pdsspect views

add_subview(subview)[source]¶

Add a ImageViewCanvas as a subview

Parameters:	subview (`ginga.qtw.ImageViewCanvasQt`) – View canvas to add as a subview
Raises:	`TypeError` – When subview is not an `ImageViewCanvas` object

cut_levels(cut_low, cut_high)[source]¶

Adjust the cut levels of the view and all the subviews

Parameters:	cut_low (`float`) – The low cut level cut_high (`float`) – The high cut level

transform(flip_x, flip_y, swap_xy)[source]¶

Apply transforms to the view and all the subviews

Parameters:	flip_x (`bool`) – Flip x axis if True. Otherwise, do not flip_y (`bool`) – Flip y axis if True. Otherwise, do not swap_xy (`bool`) – Swap the x and y axis if True. Otherwise, do not

selection¶

Window to pick selection type/color, load/export ROIs and clear ROIS

class pdsspect.selection.SelectionController(image_set, view)[source]¶

Bases: object

Controller for Selection

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model view (`Selection`) – View to control

image_set¶: PDSSpectImageSet – pdsspect model

view¶: Selection – View to control

add_ROI(coordinates, color, image_set=None)[source]¶

Add ROI with the given coordinates and color

Parameters:	coordinates (`numpy.ndarray` or `tuple`) – Either a `(m x 2)` array or a tuple of two arrays If an array, the first column are the x coordinates and the second are the y coordinates. If a tuple of arrays, the first array are x coordinates and the second are the corresponding y coordinates. color (`str`) – The name a color in `colors`

change_alpha(new_alpha)[source]¶

Change the alpha value to a new alpha value

Parameters:	new_alpha (`float`) – Value between 0 and 100

change_current_color_index(index)[source]¶

Change the current color index to a new index

Parameters:	index (`int`) – The new color index

change_selection_index(index)[source]¶

Change the selection index to a new index

Parameters:	index (`int`) – The new selection index

clear_all()[source]¶: Clear all ROIs

clear_current_color()[source]¶: Clear all the ROIs with the currently selcted color

class pdsspect.selection.Selection(image_set, parent=None)[source]¶

Bases: PyQt5.QtWidgets.QWidget, pdsspect.pdsspect_image_set.PDSSpectImageSetViewBase

Window to make/clear/load/export ROIs and choose selection mode/color

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model parent (None) – Parent of the view

image_set¶: PDSSpectImageSet – pdsspect model

parent¶: None – Parent of the view

controller¶: SelectionController – View controller

type_label¶: QtWidgets.QLabel – Label for the selection menu

selection_menu¶: QtWidgets.QComboBox – Drop down menu of selection types

type_layout¶: QtWidgets.QHBoxLayout – Horizontal box layout for selection

color_label¶: QtWidgets.QLabel – Label for the color_menu

color_menu¶: QtWidgets.QComboBox – Drop down menu for color selection

color_layout¶: QtWidgets.QHBoxLayout – Horizontal box layout for color selection

opacity_label¶: QtWidgets.QLabel – Label for the opacity_slider

opacity_slider¶: QtWidgets.QSlider – Slider to determine opacity for ROIs

opacity_layout¶: QtWidgets.QHBoxLayout – Horizontal box layout for opacity slider

clear_current_color_btn¶: QtWidgets.QPushButton – Button to clear all ROIs will the current color

clear_all_btn¶: QtWidgets.QPushButton – Button to clear all ROIs

export_btn¶: QtWidgets.QPushButton – Export ROIs to .npz file

load_btn¶: QtWidgets.QPushButton – Load ROIs from .npz file

simultaneous_roi_box¶: QtWidgets.QPushButton – When checked, new ROIs appear in every window

main_layout¶: QtWidgets.QVBoxLayout – Vertical Box layout for main layout

change_alpha(new_alpha)[source]¶: Change alpha value when opacity_slider value changes

change_color(index)[source]¶: Change the color when color selected in color_menu

change_selection_type(index)[source]¶: Change selection type when selected in selection_menu

clear_all()[source]¶: Clear all ROIs

clear_current_color()[source]¶: Clear all ROIs with current color

export(save_file)[source]¶

Export ROIS to the given filename

Parameters:	save_file (`str`) – File with `.npz` extension to save ROIs

load_selections(selected_files)[source]¶

Load ROIs from selected files

Parameters:	selected_files (`list` of `str`) – Paths to files storing ROIs

open_save_dialog()[source]¶: Open save file dialog and save rois to given filename

show_open_dialog()[source]¶: Open file dialog to select .npz files to load ROIs

transforms¶

Apply simple tranformations to the views

class pdsspect.transforms.TransformsController(image_set, view)[source]¶

Bases: object

Controller for Transforms

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model view (`Transforms`) – View to control

image_set¶: PDSSpectImageSet – pdsspect model

view¶: Transforms – View to control

set_flip_x(flip_x)[source]¶

Set flip_x

Parameters:	flip_x (`bool`) – True to flip x axis, otherwise, False

set_flip_y(flip_y)[source]¶

Set flip_y

Parameters:	flip_y (`bool`) – True to flip y axis, otherwise, False

set_swap_xy(swap_xy)[source]¶

Set swap_xy

Parameters:	swap_xy (`bool`) – True to swap x and y axis, otherwise, False

class pdsspect.transforms.Transforms(image_set, view_canvas)[source]¶

Bases: PyQt5.QtWidgets.QDialog, pdsspect.pdsspect_image_set.PDSSpectImageSetViewBase

Window to apply simple transformations

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model view_canvas (`pds_image_view_canvas.PDSImageViewCanvas`) – The view canvas to apply transformations to

image_set¶: PDSSpectImageSet – pdsspect model

view_canvas¶: pds_image_view_canvas.PDSImageViewCanvas – The view canvas to apply transformations to

controller¶: TransformsController – The view’s controller

flip_x_label¶: QtWidgets.QLabel – Label for flip_x_box

flip_x_box¶: QtWidgets.QCheckBox – Flip x axis when checked

flip_y_label¶: QtWidgets.QLabel – Label for flip_y_box

flip_y_box¶: QtWidgets.QCheckBox – Flip y axis when checked

swap_xy_label¶: QtWidgets.QLabel – Label for swap_xy_box

swap_xy_box¶: QtWidgets.QCheckBox – Swap x and y axis when checked

layout¶: QtWidgets.QGridLayout – Layout for widget

flip_x_checked(state)[source]¶

Flip x axis when checked

Parameters:	state (`int`) – The state of the checkbox (this argument is ignored and the state is checked in a more explicit way)

flip_y_checked(state)[source]¶

Flip y axis when checked

Parameters:	state (`int`) – The state of the checkbox (this argument is ignored and the state is checked in a more explicit way)

swap_xy_checked(state)[source]¶

Swap x and y axis when checked

Parameters:	state (`int`) – The state of the checkbox (this argument is ignored and the state is checked in a more explicit way)

roi¶

Region of interest creation

class pdsspect.roi.ROIBase(image_set, view_canvas, color='red', linewidth=1, linestyle='solid', showcap=False, fill=True, fillcolor=None, alpha=1.0, drawdims=False, font='Sans Serif', fillalpha=1.0, **kwargs)[source]¶

Bases: ginga.canvas.types.basic.Polygon

Base class for all ROI shapes

contains_arr(x_arr, y_arr)[source]¶

Determine whether the points in the ROI are in arrays

The arrays must be the same shape. The arrays should be result of np.mgrid[y1:y2:1, x1:x2:1]

Parameters:	x_arr (`numpy.ndarray`) – Array of x coodinates y_arr (`numpy.ndarray`) – Array of y coordinates
Returns:	result – Boolean array where coordinates that are in ROI are True
Return type:	`numpy.ndarray`

continue_ROI(data_x, data_y)[source]¶: Abstract method to continue the ROI process

create_ROI(points=None)[source]¶

Create a Region of interest

Parameters:	points (`list` of `tuple` of two `int`) – Points that make up the vertices of the ROI
Returns:	coordinates – `m x 2` array of coordinates.
Return type:	`numpy.ndarray`

static draw_after(func)[source]¶: Wrapper to redraw canvas after function

extend_ROI(data_x, data_y)[source]¶: Abstract method to extend the ROI process

lock_coords_to_pixel(data_x, data_y)[source]¶

Lock the coordinates to the bottom-left corner of the pixel

The center of the pixel has integer coordinates and the edges of the pixel are 0.5 units away. We choose to lock to the bottom left corner or each pixel. If the decimal value of the coordinate is less than or equal to 0.5 then the coordinate is to the left/below the center of the pixel. To lock we round the coordinate down and add 0.5. If the decimal value is greater than 0.5 then the coordinate is to the right/above the center. To lock we round the coordinate down and subtract 0.5. For example, if the coordinate is (2.3, 4.7) the pixel coordinate is (2, 4) and the corresponding locked coordinate is (2.5, 4.5).

Parameters:

data_x (float) – The given x coordinate
data_y (float) – The given y coordinate

Returns:

point_x (float) – The corresponding x pixel coordinate
point_y (float) – The corresponding y pixel coordinate

static lock_coords_to_pixel_wrapper(func)[source]¶: Wrapper to lock data coordinates to the corresponding pixels

right¶

float – The right edge of the image

The right edge is 0.5 units before the right edge of the image.

start_ROI(data_x, data_y)[source]¶: Abstract method to start the ROI process

stop_ROI(data_x, data_y)[source]¶: Abstract method to stop the ROI process

top¶

float – The top edge of the image

The top edge is 1.5 units past the edge of the image due to how ginga renders the image. I feel like this is a bug but I haven’t had time to try to expose it in a simple example so working around it will have to do for now.

class pdsspect.roi.Polygon(image_set, view_canvas, color='red', linewidth=1, linestyle='solid', showcap=False, fill=True, fillcolor=None, alpha=1.0, drawdims=False, font='Sans Serif', fillalpha=1.0, **kwargs)[source]¶

Bases: pdsspect.roi.ROIBase

Polygon Region of Interest

continue_ROI(data_x, data_y)[source]¶

Create new vertex on the polygon on left click

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate

extend_ROI(data_x, data_y)[source]¶

Extend the current edge of the polygon on mouse motion

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate

start_ROI(data_x, data_y)[source]¶

Start the ROI process

The ROI will be a ginga.canvas.types.basic.Path object

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate

stop_ROI(data_x, data_y)[source]¶

Close the polygon on right click

The polygon will close based on last left click and not on the right click. There must be more than 2 points to formulate a polygon

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate

class pdsspect.roi.Rectangle(image_set, view_canvas, color='red', linewidth=1, linestyle='solid', showcap=False, fill=True, fillcolor=None, alpha=1.0, drawdims=False, font='Sans Serif', fillalpha=1.0, **kwargs)[source]¶

Bases: pdsspect.roi.ROIBase

Rectangle Region of interest

extend_ROI(data_x, data_y)[source]¶

Exend the rectangle on region of interest on mouse motion

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate

start_ROI(data_x, data_y)[source]¶

Start the region of interest on left click

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate

stop_ROI(data_x, data_y)[source]¶

Stop the region of interest on right click

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate

class pdsspect.roi.Pencil(*args, **kwargs)[source]¶

Bases: pdsspect.roi.ROIBase

Select individual pixels

continue_ROI(data_x, data_y)[source]¶

Add another pixel on left click

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate

move_delta(delta_x, delta_y)[source]¶

Override the move_delta function to move all the points

Parameters:	delta_x (`float`) – Change in the x direction delta_y (`float`) – Change in the y direction

start_ROI(data_x, data_y)[source]¶

Start choosing pixels on left click

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate

stop_ROI(data_x, data_y)[source]¶

Set all pixels as roi coordinates on right click

Parameters:	data_x (`float`) – The x coordinate data_y (`float`) – The y coordinate
Returns:	coordinates – Coordinates of points selected
Return type:	`numpy.ndarray`

basic¶

class pdsspect.basic.BasicHistogramModel(*args, **kwargs)[source]¶

Bases: pdsspect.histogram.HistogramModel

Model for the hhistograms in the Basic Widgets

connected_models¶: list – Other BasicHistogramModel for other histograms

bins¶

int The number of bins the histogram uses

Setting the bins will notify the views that the bins have changed

connect_model(model)[source]¶

Connect another model to this model

model¶: BasicHistogramModel – Connect the model to current model

Raises:	`ValueError` – When `model` is not `BasicHistogramModel`

cut_high¶

float The higher cut level

Setting the high cut value will adjust the cut values in the image view and notify the views that the high cut value changed.

cut_low¶

float The lower cut level

Setting the low cut value will adjust the cut values in the image view and notify the views that the low cut value changed

cuts¶

tuple The lower and higher cut levels.

Setting the cuts will adjust the cut levels in the image viewer and notify the views that the cuts have changed. The low cut must be less than the high cut, otherwise they will be switched to satisfy that condition.

data¶: ndarray The current image data

disconnect_from_all_models()[source]¶: Disconnect all models from this model

disconnect_model(model)[source]¶

Disconnect another model from this model

model: BasicHistogramModel – Disconnect the model from current model

Raises:	`ValueError` – When `model` is not `BasicHistogramModel`

image_view¶

ImageViewCanvas The image view canvas

Setting the image view will reset the data

register(view)¶

Register a view with the model

Parameters:	view (`QtWidgets.QWidget`) – A view that utilizes this model

restore()¶: Restore the cut levels

set_data()¶: Set the data the histogram is to display

unregister(view)¶

Unregister a view with the model

Parameters:	view (`QtWidgets.QWidget`) – A view that utilizes this model

view_cuts¶: tuple The image_view cut levels

warn(title, message)¶

Display a warning box

Each view must define a warn method that returns a boolean value: True when a warning box is displayed and False when a warning box not displayed. Only one display box will be displayed. This is because multiple views should not have different handling for the same errors.

class pdsspect.basic.BasicHistogramController(model, view)[source]¶

Bases: pdsspect.histogram.HistogramController

Controller for histogram views

Parameters:	model (`BasicHistogramModel`) – histogram model view (`object`) – View with `BasicHistogramModel` as its model

model¶: BasicHistogramModel – histogram model

view¶: object – View with BasicHistogramModel as its model

restore()[source]¶: Restore the histogram

set_cut_high(cut_high)[source]¶

Set the high cut level to a new value

Parameters:	cut_high (`float`) – New high cut value

set_cut_low(cut_low)[source]¶

Set the low cut level to a new value

Parameters:	cut_low (`float`) – New low cut value

set_cuts(cut_low, cut_high)[source]¶

Set both the low and high cut levels

Parameters:	cut_low (`float`) – New low cut value cut_high (`float`) – New high cut value

class pdsspect.basic.BasicHistogramWidget(*args, **kwargs)[source]¶

Bases: pdsspect.histogram.HistogramWidget

HistogramWidget in a different layout

class pdsspect.basic.BasicController(image_set, view)[source]¶

Bases: object

Controller for Basic window

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model view (`Basic`) – View to control

image_set¶: PDSSpectImageSet – pdsspect model

view¶: Basic – View to control

change_current_image_index(new_index)[source]¶

Change the current image index to a new index

Parameters:	new_index (`int`) – The new index for `images` to determine the current image

class pdsspect.basic.BasicWidget(image_set, view_canvas)[source]¶

Bases: PyQt5.QtWidgets.QWidget

Widget to hold each basic window

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model view_canvas (`PDSImageViewCanvas`) – view canvas

image_set¶: PDSSpectImageSet – pdsspect model

basics¶: list of Basic – Basic in the widget

add_basic(image_set, view_canvas)[source]¶

Add a Basic to the widget

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model view_canvas (`PDSImageViewCanvas`) – view canvas

connect_model(basic)[source]¶

Connect the models of other basic windows to the given window

The models are connected when they have the same current image

Parameters:	basic (`Basic`) – Basic window connect/disconnect its histogram model to others

class pdsspect.basic.Basic(image_set, view_canvas, basic_widget)[source]¶

Bases: PyQt5.QtWidgets.QWidget, pdsspect.pdsspect_image_set.PDSSpectImageSetViewBase

Window to apply cut levels and choose the current image

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model view_canvas (`PDSImageViewCanvas`) – Canvas to view the image

image_set¶: PDSSpectImageSet – pdsspect model

view_canvas¶: PDSImageViewCanvas – Canvas to view the image

controller¶: BasicController – Controller for view

image_menu¶: QtWidgets.QComboBox – Drop down menu to pick the current image

histogram¶: HistogramModel – Model for the histogram_widget

histogram_widget¶: BasicHistogramWidget – The histogram widget to adjust the cut levels

layout¶: QtWidgets.QVBoxLayout – The main layout

change_image(new_index)[source]¶

Change the image when new image selected in image_menu

Parameters:	new_index (`int`) – The new index to determine the current image

set_image()[source]¶: When the image is set, adjust the histogram

histogram¶

class pdsspect.histogram.HistogramModel(image_view, cut_low=None, cut_high=None, bins=100)[source]¶

Bases: object

Model for a Histogram which can apply cut levels to an image

Any View that utilizes this model must define the following methods: set_data, change_cut_low, change_cut_high, change_cuts, warn, and change_bins. The warn method must return a boolean and if more than one view utilizes this model, you should consider only one actually creating a warning box and return True while the others just return False.

Parameters:	image_view (`ImageViewCanvas`) – The image view canvas cut_low (`float`) – The lower cut level cut_high (`float`) – The higher cut level bins (`int`) – The number of bins the histogram uses

bins¶

int The number of bins the histogram uses

Setting the bins will notify the views that the bins have changed

cut_high¶

float The higher cut level

Setting the high cut value will adjust the cut values in the image view and notify the views that the high cut value changed.

cut_low¶

float The lower cut level

Setting the low cut value will adjust the cut values in the image view and notify the views that the low cut value changed

cuts¶

tuple The lower and higher cut levels.

Setting the cuts will adjust the cut levels in the image viewer and notify the views that the cuts have changed. The low cut must be less than the high cut, otherwise they will be switched to satisfy that condition.

data¶: ndarray The current image data

image_view¶

ImageViewCanvas The image view canvas

Setting the image view will reset the data

register(view)[source]¶

Register a view with the model

Parameters:	view (`QtWidgets.QWidget`) – A view that utilizes this model

restore()[source]¶: Restore the cut levels

set_data()[source]¶: Set the data the histogram is to display

unregister(view)[source]¶

Unregister a view with the model

Parameters:	view (`QtWidgets.QWidget`) – A view that utilizes this model

view_cuts¶: tuple The image_view cut levels

warn(title, message)[source]¶

Display a warning box

Each view must define a warn method that returns a boolean value: True when a warning box is displayed and False when a warning box not displayed. Only one display box will be displayed. This is because multiple views should not have different handling for the same errors.

class pdsspect.histogram.HistogramController(model, view)[source]¶

Bases: object

Controller for histogram views

Parameters:	model (`HistogramModel`) – histogram model view (`object`) – View with `HistogramModel` as its model

model¶: HistogramModel – histogram model

view¶: object – View with HistogramModel as its model

restore()[source]¶: Restore the histogram

set_bins(bins)[source]¶

Change the number of bins the histogram uses

Parameters:	bins (`int`) – The number number of bins for the histogram

set_cut_high(cut_high)[source]¶

Set the high cut level to a new value

Parameters:	cut_high (`float`) – New high cut value

set_cut_low(cut_low)[source]¶

Set the low cut level to a new value

Parameters:	cut_low (`float`) – New low cut value

set_cuts(cut_low, cut_high)[source]¶

Set both the low and high cut levels

Parameters:	cut_low (`float`) – New low cut value cut_high (`float`) – New high cut value

class pdsspect.histogram.HistogramWidget(model, parent=None)[source]¶

Bases: PyQt5.QtWidgets.QWidget

View to display the histogram with text boxes for cuts and bins

Parameters:	model (`HistogramModel`) – The view’s model

model¶: HistogramModel – The view’s model

controller¶: HistogramController – The view’s controller

histogram¶: Histogram – The histogram itself

change_bins()[source]¶: Change the bins box text

change_cut_high()[source]¶: Set the high cut box text

change_cut_low()[source]¶: Set the low cut box text

change_cuts()[source]¶: Set the low and high cut boxes’ text

keyPressEvent(event)[source]¶: When the enter button is pressed, adjust the cut levels and bins

warn(title, message)[source]¶: Displayed a timed message box the warning

class pdsspect.histogram.Histogram(model)[source]¶

Bases: matplotlib.backends.backend_qt5agg.FigureCanvasQTAgg

The Histogram View

Parameters:	model (`HistogramModel`) – The view’s model

model¶: HistogramModel – The view’s model

controller¶: HistogramController – The view’s controller

change_bins()[source]¶: Adjust the number of bins without adjusting the lines

change_cut_high(draw=True)[source]¶: Change the position of the right line to the high cut level

change_cut_low(draw=True)[source]¶: Change the position of the left line to the low cut level

change_cuts()[source]¶: Change the position of the left & right lines to respective cuts

set_data(reset_vlines=True)[source]¶

Set the histogram’s data

Parameters:	reset_vlines (`bool`) – Reset the vertical lines to the default cut levels if True, otherwise False. True by default

roi_plot¶

Parent classes for any widget that plots data

class pdsspect.roi_plot.ROIPlotModel(image_set)[source]¶

Bases: object

Model for ROI Plot and accompanying widget

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model

selected_colors¶: list – Colors to display in the histogram

latex_units¶: list of 3 str – The latex strings of pdsspect_image_set.PDSSpectImageSet.accepted_units

add_selected_color(color)[source]¶

Select a color and inform views to display new color

Parameters:	color (`str`) – The color to add

has_multiple_views¶: bool – True if there are multiple views, False otherwise

image_set¶: PDSSpectImageSet – Image set that corresponds with the current view

image_sets¶: list – All the image sets, including the current one

register(view)[source]¶: Register view with the model

remove_selected_color(color)[source]¶

Remove a selected color and inform views to not display the color

Parameters:	color (`str`) – The color to remove

unit¶: str – Latex version of pdsspect_image_set.PDSSpectImageSet.unit

unregister(view)[source]¶: Unregister view with the model

view_index¶

int – The index of the view to display the ROI data

If there are not multiple views, view_index is automatically -1.

class pdsspect.roi_plot.ROIPlotController(model, view)[source]¶

Bases: object

Controller for ROI plot and accompanying widget

Parameters:	model (`ROIPlotModel`) – The model view (`QtWidgets.QWidget`) – The view

model¶: ROIPlotModel – The model

view¶: QtWidgets.QWidget – The view

color_state_changed(color)[source]¶

Select or remove the color when a checkbox color changes

Parameters:	color (`str`) – The name of the checkbox whose state changed

remove_color(color)[source]¶

Remove a given color

Parameters:	color (`str`) – The color to remove

select_color(color)[source]¶

Selected a given color

Parameters:	color (`str`) – The color to select

set_view_index(index)[source]¶

Set the index of the view

Parameters:	index (`int`) – Index of the view

class pdsspect.roi_plot.ROIPlotWidget(model)[source]¶

Bases: PyQt5.QtWidgets.QWidget, pdsspect.pdsspect_image_set.PDSSpectImageSetViewBase

Widget to hold the histogram and checkboxs

Checkboxes are created in create_color_checkbox() which is why they do not appear in the __init__() method.

Parameters:	model (`ROIPlotModel`) – The model

model¶: ROIPlotModel – The model

controller¶: ROIPlotController – The controller

checkbox_layout¶: QtWidgets.QVBoxLayout – Place the checkboxes vertically

main_layout¶: QtWidgets.QGridLayout – Place in grid layout so histogram stretches while boxes are stationary

roi_plot¶: ROIPlot – The plot of ROI data

save_btn¶: QtWidgets.QPushButton – Save the plot as an image

red_checkbox¶: ColorCheckBox – Red checkbox that displays red ROI data when checked

brown_checkbox¶: ColorCheckBox – Brown checkbox that displays brown ROI data when checked

lightblue_checkbox¶: ColorCheckBox – Lightblue checkbox that displays lightblue ROI data when checked

lightcyan_checkbox¶: ColorCheckBox – Lightcyan checkbox that displays lightcyan ROI data when checked

darkgreen_checkbox¶: ColorCheckBox – Darkgreen checkbox that displays darkgreen ROI data when checked

yellow_checkbox¶: ColorCheckBox – Yellow checkbox that displays yellow ROI data when checked

pink_checkbox¶: ColorCheckBox – Pink checkbox that displays pink ROI data when checked

teal_checkbox¶: ColorCheckBox – Teal checkbox that displays teal ROI data when checked

goldenrod_checkbox¶: ColorCheckBox – Goldenrod checkbox that displays goldenrod ROI data when checked

sienna_checkbox¶: ColorCheckBox – Sienna checkbox that displays sienna ROI data when checked

darkblue_checkbox¶: ColorCheckBox – Darkblue checkbox that displays darkblue ROI data when checked

crimson_checkbox¶: ColorCheckBox – Crimson checkbox that displays crimson ROI data when checked

maroon_checkbox¶: ColorCheckBox – Maroon checkbox that displays maroon ROI data when checked

purple_checkbox¶: ColorCheckBox – Purple checkbox that displays purple ROI data when checked

add_view(index=None)[source]¶

Add a view box to the widget

Parameters:	index (`int` [Default None]) – The index to add the view to

check_color(checkbox_color)[source]¶

Called when the state a checkbox is changed

Parameters:	checkbox_color (`str`) – The color label of the check box

check_view_checkbox(view_checkbox)[source]¶

Check the view box at the given index

Parameters:	view_checkbox (`ViewCheckBox`) – The view check box whose state changed

create_color_checkbox(color)[source]¶

Create a checkbox with the given color

Parameters:	color (`str`) – The color to name the checkbox

save_plot()[source]¶: Save the plot as an image

class pdsspect.roi_plot.ROIPlot(model)[source]¶

Bases: matplotlib.backends.backend_qt5agg.FigureCanvasQTAgg, pdsspect.pdsspect_image_set.PDSSpectImageSetViewBase

Plot of the data in each ROI color

Parameters:	model (`ROIPlotModel`) – The model image_set (`PDSSpectImageSet`) – pdsspect model

model¶: ROIPlotModel – The model

image_set¶: PDSSpectImageSet – pdsspect model

set_roi_data()[source]¶: Set data when ROI is created/destroyed or checkbox is toggled

class pdsspect.roi_plot.ColorCheckBox(color)[source]¶

Bases: PyQt5.QtWidgets.QCheckBox

Custom checkbox that emits its color (str) when toggled

Parameters:	color (`str`) – The color to name the checkbox

color¶: str – The color to name the checkbox

stateChanged¶

QtCore.Signal – Signal that emits a string when check box changes its state

roi_histogram¶

class pdsspect.roi_histogram.ROIHistogramModel(image_set)[source]¶

Bases: pdsspect.roi_plot.ROIPlotModel

Model for ROI histogram and accompanying widget

add_selected_color(color)¶

Select a color and inform views to display new color

Parameters:	color (`str`) – The color to add

compare_data¶: bool – True if image_index is not -1

has_multiple_views¶: bool – True if there are multiple views, False otherwise

image_index¶

int – The index of the image to which to compare data with

When setting image_index, it may be changed to -1 if the image is the same as the current image. Furthermore, when setting the view_index, the image_index may be changed to -1 if the view_index and the current_image_index are the same.

image_set¶: PDSSpectImageSet – Image set that corresponds with the current view

image_sets¶: list – All the image sets, including the current one

register(view)¶: Register view with the model

remove_selected_color(color)¶

Remove a selected color and inform views to not display the color

Parameters:	color (`str`) – The color to remove

unit¶: str – Latex version of pdsspect_image_set.PDSSpectImageSet.unit

unregister(view)¶: Unregister view with the model

view_index¶

int – The index of the view to display the ROI data

If there are not multiple views, view_index is automatically -1.

xdata(color)[source]¶

Data inside a ROI with the given color for the current image

Parameters:	color (`str`) – The color of the ROI
Returns:	data – Data in ROI color for the xaxis
Return type:	`numpy.ndarray`

xlim¶: list of two float – min max of current image’s data

ydata(color)[source]¶

Data inside a ROI with the given color for the image in the menu

Parameters:	color (`str`) – The color of the ROI
Returns:	data – Data in ROI color for the yaxis
Return type:	`numpy.ndarray`

ylim¶: list of two float – min max of yaxis image

class pdsspect.roi_histogram.ROIHistogramController(model, view)[source]¶

Bases: pdsspect.roi_plot.ROIPlotController

Controller for ROI histogram and accompanying widget

Parameters:	model (`ROIHistogramModel`) – The model view (`ROIHistogramWidget` or `ROIHistogram`) – The view

model¶: ROIHistogramModel – The model

view¶: ROIHistogramWidget or ROIHistogram – The view

color_state_changed(color)¶

Select or remove the color when a checkbox color changes

Parameters:	color (`str`) – The name of the checkbox whose state changed

remove_color(color)¶

Remove a given color

Parameters:	color (`str`) – The color to remove

select_color(color)¶

Selected a given color

Parameters:	color (`str`) – The color to select

set_image_index(index)[source]¶

Set the index of the image in the menu

Parameters:	index (`int`) – Index of the image menu

set_view_index(index)¶

Set the index of the view

Parameters:	index (`int`) – Index of the view

class pdsspect.roi_histogram.ROIHistogramWidget(model)[source]¶

Bases: pdsspect.roi_plot.ROIPlotWidget

Widget to hold the histogram and check boxes

Parameters:	model (`ROIHistogramModel`) – The model

model¶: ROIHistogramModel – The model

controller¶: ROIHistogramController – The controller

image_menu¶: QtWidgets.QComboBox – Menu to select image for y axis

select_image(index)[source]¶

Select an image when image is selected in the menu

Parameters:	index (`int`) – The index of the selected image

class pdsspect.roi_histogram.ROIHistogram(model)[source]¶

Bases: pdsspect.roi_plot.ROIPlot

Histogram view of the data in each ROI color

Parameters:	model (`ROIHistogramModel`) – The model

model¶: ROIHistogramModel – The model

set_data()[source]¶: Set the data of the selected colors on the histogram

set_image()[source]¶: Set data when image is changed

roi_line_plot¶

class pdsspect.roi_line_plot.ROILinePlotModel(image_set)[source]¶

Bases: pdsspect.roi_plot.ROIPlotModel

Model for ROI Line plot and widget

add_selected_color(color)¶

Select a color and inform views to display new color

Parameters:	color (`str`) – The color to add

data_with_color(color)[source]¶

Get the data inside the ROI color if the image has a wavelength

Parameters:	color (`str`) – The color of the ROI
Returns:	data – Sorted list of arrays of data by wavelength
Return type:	`list` or `numpy.ndarray`

has_multiple_views¶: bool – True if there are multiple views, False otherwise

image_set¶: PDSSpectImageSet – Image set that corresponds with the current view

image_sets¶: list – All the image sets, including the current one

register(view)¶: Register view with the model

remove_selected_color(color)¶

Remove a selected color and inform views to not display the color

Parameters:	color (`str`) – The color to remove

unit¶: str – Latex version of pdsspect_image_set.PDSSpectImageSet.unit

unregister(view)¶: Unregister view with the model

view_index¶

int – The index of the view to display the ROI data

If there are not multiple views, view_index is automatically -1.

wavelengths¶: list – Sorted list of wavelengths in the image_set

class pdsspect.roi_line_plot.ROILinePlotController(model, view)[source]¶

Bases: pdsspect.roi_plot.ROIPlotController

Controller for ROILinePlotWidget

color_state_changed(color)¶

Select or remove the color when a checkbox color changes

Parameters:	color (`str`) – The name of the checkbox whose state changed

remove_color(color)¶

Remove a given color

Parameters:	color (`str`) – The color to remove

select_color(color)¶

Selected a given color

Parameters:	color (`str`) – The color to select

set_view_index(index)¶

Set the index of the view

Parameters:	index (`int`) – Index of the view

class pdsspect.roi_line_plot.ROILinePlotWidget(model)[source]¶

Bases: pdsspect.roi_plot.ROIPlotWidget

Widget to hold line plot and check boxes

Parameters:	model (`ROILinePlotModel`) – The model

model¶: ROILinePlotModel – The model

controller¶: ROILinePlotController – The controller

class pdsspect.roi_line_plot.ROILinePlot(model)[source]¶

Bases: pdsspect.roi_plot.ROIPlot

Line plot of ROI data

Parameters:	model (`ROILinePlotModel`) – The model

model¶: ROILinePlotModel – The model

set_data()[source]¶: Set the data of the selected colors on the line plot

set_wavelength¶

class pdsspect.set_wavelength.SetWavelengthModel(image_set)[source]¶

Bases: object

Model for SetWavelengthWidget

Parameters:	image_set (`PDSSpectImageSet`) – pdsspect model

image_set¶: PDSSpectImageSet – pdsspect model

accepted_units¶: list – List of accepted units – nm, um, and AA

current_image¶: ImageStamp – Current image in menu

current_image_index¶: int – Index of current image in menu

display_current_wavelength()[source]¶: Display current wavelength in registered views

unit¶

str – image_set unit

Setting the :attr`unit` will set the image_set unit

unit_index¶: int Index of – attr`unit` in accepted_units

class pdsspect.set_wavelength.SetWavelengthController(model, view)[source]¶

Bases: object

Controller for SetWavelengthWidget

Parameters:	model (`SetWavelengthModel`) – Model for `SetWavelengthWidget` view (`SetWavelengthWidget`) – The view to control

model¶: SetWavelengthModel – Model for SetWavelengthWidget

view¶: SetWavelengthWidget – The view to control

change_unit(index)[source]¶

Set the model’s SetWavelengthModel.unit

Parameters:	index (`int`) – Index of `SetWavelengthModel.accepted_units` to change the `SetWavelengthModel.unit` to

set_current_image_index(index)[source]¶

Set the model’s SetWavelengthModel.current_image_index

Parameters:	index (`int`) – Index to change `SetWavelengthModel.current_image_index` to

set_image_wavelength(wavelength)[source]¶

Set the model’s SetWavelengthModel.current_image wavelength

Parameters:	wavelength (`float`) – The model’s `SetWavelengthModel.current_image` new wavelength

class pdsspect.set_wavelength.SetWavelengthWidget(model)[source]¶

Bases: PyQt5.QtWidgets.QMainWindow

Widget to set images wavelength

Using a QtWidgets.QMainWindow for the status bar at the bottom.

Parameters:	model (`SetWavelengthModel`) – Model for `SetWavelengthWidget`

model¶: SetWavelengthModel – Model for SetWavelengthWidget

controller¶: SetWavelengthController – The widgets controller

image_menu¶: QtWidgets.QComboBox – Menu to choose the image to set the wavelength

wavelength_text¶: QtWidgets.QLineEdit – Text box to enter and display wavelength

units_menu¶: QtWidgets.QComboBox – Menu to choose unit of wavelength

main_layout¶: QtWidgets.QHBoxLayout – Main layout of widget

change_unit(index)[source]¶

Change SetWavelengthModel.unit to unit in units_menu

Parameters:	index (`int`) – Index of `SetWavelengthModel.accepted_units` to change the `SetWavelengthModel.unit` to

display_current_wavelength()[source]¶: Display the SetWavelengthModel.current_image wavelength in wavelength_text

select_image(index)[source]¶

Select current image

Parameters:	index (`int`) – Index to change `SetWavelengthModel.current_image_index` to

set_wavelength()[source]¶: Set the SetWavelengthModel.current_image wavelength to value in wavelength_text

show_status_bar_wavelength_set()[source]¶: Alert user wavelength is set

Instrument Models¶

Supported Instruments¶

MER
- Pancam
MSL
- Mastcam
Cassini
- Imaging Science Subsystem (ISS)

get_wavelength¶

Get the wavelength from an image’s label

instrument_models.get_wavelength.get_wavelength(label, unit)[source]¶

Get the filter wavelength from the label of an image

See Supported Instruments for full list of supported missions and instruments. If the instrument is not supported, get_wavelength() will return nan.

Parameters:

label (pvl.PVLModule) – Image’s label
unit (str [nm]) – The wavelength unit. Best practice for unit to exist in pdsspect.pdsspect_image_set.ImageStamp.accepted_units

Returns:

wavelength – The filter wavelenth from the image rounded to 3 decimal places.

If image does not have a wavelength or the instrument is not supported, wavelength with be nan

Return type:

float

instrument¶

Provide base class for all instrument models

class instrument_models.instrument.InstrumentBase(label)[source]¶

Abstract Base Class for all instrument models

Parameters:	label (`pvl.PVLModule`) – Image’s label

label¶: pvl.PVLModule – Image’s label

get_wavelength(unit, *args, **kwargs)[source]¶

Abstract method to get the image’s wavelength

Parameters:	unit (`str` [`nm`]) – The wavelength unit. Best practice for `unit` to exist in `pdsspect.pdsspect_image_set.ImageStamp.accepted_units`
Returns:	wavelength – The image’s filter wavelength
Return type:	`float`

mastcam¶

class instrument_models.mastcam.Mastcam(label)[source]¶

Bases: instrument_models.instrument.InstrumentBase

Model to get the filter wavelength of a Mastcam image

See Mastcam Multispectral Imaging on the Mars Science Laboratory Rover: Wavelength Coverage and Imaging Strategies at the Gale Crater Field Site for more details on Mastcam’s filter wavelengths

group¶: str – INSTRUMENT_STATE_PARMS

wavelength_key1¶: str – CENTER_FILTER_WAVELENGTH

wavelength_key2¶: str – FILTER_CENTER_WAVELENGTH

get_wavelength(unit='nm')[source]¶

Get the wavelength from mastcam image

Parameters:	unit (`str` [`nm`]) – The wavelength unit. Best practice for `unit` to exist in `pdsspect.pdsspect_image_set.ImageStamp.accepted_units`
Returns:	wavelength – Filter wavelength of the mastcam image
Return type:	`float`

pancam¶

class instrument_models.pancam.Pancam(label)[source]¶

Bases: instrument_models.instrument.InstrumentBase

Model to get the filter wavelength of a Patcam image

See Pancam for more details on Pancam’s filter wavelengths.

pancam_left¶: str – PANCAM_LEFT

pancam_right¶: str – PANCAM_RIGHT

unit¶: str – nm

left_filters¶: dict – Key is the filter number and the value is the wavelength for PancamL

right_filters¶: dict – Key is the filter number and the value is the wavelength for PancamR

camera¶: bool – Images camera. Should either be left_filters or right_filters

filter_num¶: int – The images filter number

get_wavelength(unit='nm')[source]¶

Get the filter wavelength from the image

Parameters:	unit (`str` [`nm`]) – The wavelength unit. Best practice for `unit` to exist in `pdsspect.pdsspect_image_set.ImageStamp.accepted_units`
Returns:	wavelength – The image’s filter wavelength
Return type:	`float`

is_left¶: bool – True if image is from Pancam Left

is_right¶: bool – True if image is from Pancam Right

cassini_iss¶

class instrument_models.cassini_iss.CassiniISS(label)[source]¶

Bases: instrument_models.instrument.InstrumentBase

Model to get the filter wavelength from Cassini ISS image

See Cassini Imaging Science Subsystem (ISS) Data User’s Guide (Page 149) for table of filter name and corresponding wavelengths. We use the effective wavelength rather than the center wavelength.wavelength

NA_filters¶

dict – Dictionary of the ISS Narrow Angle Camera filter names and wavelengths

Key is the two filternames and the value is the wavelength in nm

WA_filters¶

dict – Dictionary of the ISS Wide Angle Camera filter names and wavelengths

Key is the two filternames and the value is the wavelength in nm

unit¶: str – The default unit is nm

filter_name¶

str – The image’s filter names joined by a comma and space

For example, in the label the filtername appears as ("CL1","UV3") and so filter_name returns 'CL1, UV3'

get_wavelength(unit='nm')[source]¶

Get the image’s filter wavelength

Parameters:	unit (`str` [`nm`]) – The desired wavelength of the unit
Returns:	wavelength – The image’s filter wavelength rounded to 3 decimal places
Return type:	`float`

is_NA¶: bool – True if image is from Narrow Angle Camera

is_WA¶: bool – True if image is from Wide Angle Camera

Contributing¶

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given. To understand and better read the code, you should have an understanding of the Model-View-Controller (MVC) architecture.

You can contribute in many ways:

Types of Contributions¶

Report Bugs¶

Report bugs at https://github.com/planetarypy/pdsspect/issues.

If you are reporting a bug, please include:

Your operating system name and version.
Any details about your local setup that might be helpful in troubleshooting.
Detailed steps to reproduce the bug.

Fix Bugs¶

Look through the GitHub issues for bugs. Anything tagged with “bug” is open to whoever wants to implement it.

Implement Features¶

Look through the GitHub issues for features. Anything tagged with “feature” is open to whoever wants to implement it.

Write Documentation¶

pdsspect could always use more documentation, whether as part of the official pdsspect docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback¶

The best way to send feedback is to file an issue at https://github.com/planetarypy/pdsspect/issues.

If you are proposing a feature:

Explain in detail how it would work.
Keep the scope as narrow as possible, to make it easier to implement.
Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!¶

Ready to contribute? Here’s how to set up pdsspect for local development.

Fork the pdsspect repo on GitHub.

Clone your fork locally:

$ git clone git@github.com:your_name_here/pdsspect.git

Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
```
$ mkvirtualenv pdsspect
$ cd pdsspect/
$ pip install -r requirements.txt
```
Create a branch for local development:
```
$ git checkout -b name-of-your-bugfix-or-feature
```
Now you can make your changes locally.
When you’re done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:
```
$ make lint
$ make test
$ make test-all
```
To get flake8 and tox, just pip install them into your virtualenv.

Commit your changes and push your branch to GitHub:

$ git add .
$ git commit -m "Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature

Submit a pull request through the GitHub website.

Pull Request Guidelines¶

Before you submit a pull request, check that it meets these guidelines:

The pull request should include tests.
If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
The pull request should work for Python 2.6, 2.7, 3.3, and 3.4, and for PyPy. Check https://travis-ci.org/planetarypy/pdsspect/pull_requests and make sure that the tests pass for all supported Python versions.

Tips¶

To run a subset of tests:

py.test tests/

Credits¶

Development Lead¶

PlanetaryPy Developers <contact@planetarypy.com>

Contributors¶

Perry Vargas <perrybvargas@gmail.com>
Austin Godber <godber@uberhip.com>

History¶

0.1.1 (“2017-08-21”)¶

Make compatible to be opened by other programs like pystamps

0.1.0 (“2017-08-20”)¶

First release on PyPi

Welcome to pdsspect’s documentation!¶

pdsspect - A Python PDS Image Region of Interest Selection Tool¶

Features¶

Install¶

Install Using Pip¶

Install for Development¶

Quick Tutorial¶

Images In Example¶

Supported Instruments¶

Adding More Instruments¶

Pull Request Checklist¶

Style¶

pdsspect¶

pdsspect_image_set¶

pdsspect_view¶

pan_view¶

pds_image_view_canvas¶

selection¶

transforms¶

roi¶

basic¶

histogram¶

roi_plot¶

roi_histogram¶

roi_line_plot¶

set_wavelength¶

Instrument Models¶

Supported Instruments¶

get_wavelength¶

instrument¶

mastcam¶

pancam¶

cassini_iss¶

Contributing¶

Types of Contributions¶

Report Bugs¶

Fix Bugs¶

Implement Features¶

Write Documentation¶

Submit Feedback¶

Get Started!¶

Pull Request Guidelines¶

Tips¶

Credits¶

Development Lead¶

Contributors¶

History¶

0.1.1 (“2017-08-21”)¶

0.1.0 (“2017-08-20”)¶

Indices and tables¶