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Name	Modified	Size
PhenalysisInstaller_web.exe	2019-08-28	75.3 MB
Readme.md	2019-04-15	9.5 kB
Totals: 2 Items		75.3 MB

Requirements

Phenalysis is a MATLAB application which can run without installing MATLAB. It requires MATLAB Runtime which is automatically downloaded from the web during installation.

Please refer to the Windows system requirements

User Guide

Quick video tutorials.

Importing a raster image

Overlaying a grid

Computing a vegetation index

Refining grid position

Interface

Browser panel

Browse button

Opens a dialog box to import files.

Click on the … button to display the file import dialog.
Choose the file extension filter to view compatible formats.
Locate and select a file and click Open.

Tip: Open a raster image stored in separate files (e.g. multispectral image) by selecting multiple files and clicking Open.

Address bar

Displays the path of the current folder. Edit to set a different path.

💡 Press▾to select a recently used folder location.

⚠️Entering an invalid path throws a warning and reverts to the previous path.

Folder list

Displays the contents of the current folder.

Double click an item from the list to open the Import as dialog.
Select appropriate import format from the list and press OK.

💡 Open a raster image stored in separate files (e.g. multispectral image) by holding the Ctrl key while selecting files and then press Enter.

⚠️The list does not refresh dynamically.

Layers panel

Loading a raster image creates a new layer named from the filename. Loading another raster adds a layer on top of the previous layer, and so on.

💡 Select a layer by clicking on its name in the Layers panel. Select a range of layers by holding the Shift key, or the Ctrl key to select layers in any order.

💡 Toggle layer visibility via the checkbox besides its name.

💡 Toggle raster image visibility using ▢ icon in the top right corner of the view panel.

Raster and Vector tabs reflect information of the last selected layer.

Right click in the layers panel opens a context menu with the following options:

Shift shift the selected layer(s) within the front-to-back visual stacking order.

Select the layer(s) to shift.
Right click and select Shift from the context menu, and choose one of the functions:
- Top: bring layer to top.
- Up: bring layer one step forward.
- Down: send layer one step backward.
- Bottom: send layer to bottom.

Index compute a vegetation index from the raster image of selected layer(s).

Select the layer(s) to compute vegetation index.
Right click and select Index from the context menu.
Choose from the list of indices and press OK.
Optionally customize the Name and Formula using (case-insensitive) names of bands and press OK.

⚠️ Bands expressed in a formula must also be designated in the raster image.

💡 Toggle index visibility using ✾ icon in the top right corner of the view panel.

Crop crop the raster in selected layer(s) to a selected region.

Select the layer(s) to crop.
Right click and select Crop from the context menu.
Click and drag in the view panel to specify the region.

Register geometrically register raster images of selected layers based on control points.

Place at least 4 control points on the raster of each layer.
Select at least 2 layers to register.
Right click and select Register from the context menu.

Raster image is warped according to geometric transformation computed using the control points.

Color change color associated with the vector data (e.g. grid, points) of selected layer(s).

Select the layer(s) to change the associated color.
Right click and select Color from the context menu.
Choose a color from the color picker and click OK.

Note: Colors cycle through a 7-color pallete for every new layer.

Rename change name of a layer.

Select the layer to rename.
Right click and select Rename from the context menu.
Modify the layer name and press Enter.

Remove delete the selected layer(s).

Select the layer(s) to remove.
Right click and select Remove from the context menu.

Raster tab

Contains information about spatial referencing and visual rendering of the raster image.

Reference panel

Geogrpahic referencing parameters of the raster image. Geo-referencing information is automatically read from the TIFF metadata (if present) or from a corresponding TFW world file (if exists).

RasterSize: Number of columns/rows of the image. Editing this value resizes the image.
CellExtent: Extent in world x,y coordinates of individual pixels.
RasterExtent: Extent of the full image as measured in the world system in a direction parallel to its rows and columns.
Limits: Limits of raster in world coordinates.
IndexStartFrom: Edge from which row/column indexing starts. Replace North/South, East/West to correct cardinal direction.

⤓ save raster image of selected layer in the specified format.

Select the layer from which to save the raster image.
Press ⤓ to open the save image dialog.
Enter Filename and set appropriate format in the Save as type field.
Click Save.

⚠️ Rendering effects are not preserved in the saved image.

Rendering panel

Specifies the rendering method and parameters of the raster image.

Method dropdown menu provides option to specify a method of rendering the raster image.

truecolor: Image of 1 grayscale or 3 channels designated as red, green, blue.
falsecolor: Image with at least 3 channels designated as blue, green, red; rendered in RGB colors.
pseudocolor: Image with at least 1 channel; rendered in selected pseudo color map.

Channels table shows in the order of image channels:

band: Name of channel. Edit to change band association.
min: Minimum valid pixel value of channel. Edit to specify a different minimum value.
max: Maximum valid pixel value of channel. Edit to specify a different maximum value.

[x] Clip saturated pixels using threshold (Γ) and apply nonlinear mapping factor (γ)

Γ₋: percentage of low saturated pixels (0<Γ₋≪Γ₊)
Γ₊: percentage of high saturated pixels (Γ₋≪Γ₊< 100)
↕: links Γ₋ and Γ₊ values such that their sum is constant (Γ₋+Γ₊=100)
γ: nonlinear mapping factor, γ>1 (brighter), γ< 1 (darker)

Vector tab

Provides option to overlay spatial data (grid or points) on a raster image.

Grid panel

Provides option to overlay a grid of rectangular cells and control its specficiations.

⌖ draw grid interactively.

Press the ⌖ button to enable drawing mode.
Click and drag on the raster image to place grid in the view panel.
Depress the ⌖ button to disable drawing mode.

The following interactive commands are acceptable to manipulate a grid.

Left click: translate grid
Right click (or hold Ctrl key with left click): rotate grid
Middle click (or hold Shift key with left click): scale grid
Double click (or simultaneous left click and right click): shift cell spacing

💡 Change grid specifications from the table or interactively manipulate the grid in the view panel.

⤓ save grid in MATLAB (.mat) or Shapefile (.shp) format.

⚠️ Shapefiles are not compatible for importing.

◰◳◱◲: Anchor of the grid, north-west, north-east, south-west or south-east.
→,← ↓,↑: Direction of cell sequence, row first or column first.
⇉,⇊,⇇,⇈ ⇄,⇵,⇆,⇅: Pattern of cell sequence, zig-zag or serpentine
▦ ◽: Mode of interaction, grid or cell.

Dimensions panel specifies physical dimensions of the grid.

⊾°: Rotation angle of the grid (in degrees) about the anchor.
cells: Number of cells in each dimension.
origin: Position of the anchor in world coordinates.
size: Width and height of each cell in world coordinates.
space: Distance between cells in world coordinates.

Refine panel provides option to refine and reset position of grid cells with following specification

▸ Refines the position of grid cells.

cells: Number of cells in each dimension to refine as a group.
Δsiz.: (experimental) Cell size allowance as a fraction of width and height of the cells. (0-1)
Δspc.: Cell position allowance as a fraction of distance between cells. (0-1)

⟲ Resets the grid cell positions to initial state.