Customized Import Dialog Box
13. To load an import template to the Customized Import dialog box, click the Load button j . Note that the Root Folder and Sample File are not defined to allow the
usage as import template.
Image Layers Import Options
On the Image Layers tab of the Customized Import dialog box, you can configure image layers of scenes to be imported. That way, you modify the import template
Image Layers Import Options on page 67 Thematic Layers Import Options on page 70 Metadata Import Options on page 72 Metadata Import Options on page 72
Import Scenes to a Workspace on page 59
concerning the following options:
• Add image files.
• Remove image layers and image files.
• Define a special search string for files.
• Select image format driver for importing.
• Modify image layer aliases.
• Define No-data handling.
Preconditions:
• Define a master file on the Workspace tab. Without a master file, you cannot access the Image Layers tab.
• Before modifying the image layer options, we recommend that you first test the customized import with the default settings of the Workspace tab.
Figure 46: Image Layers tab of the Customized Import dialog box.
1. The Image Layers tab lists the Files to be imported with the included image Layers. Image layers are sequenced according to their Channel number.
2. To add files, click the Add File button.
3. To remove a file, select it and click the Remove File button. You cannot remove the last remaining file.
4. To remove a image layer, select it and click the Remove Layer button. You cannot remove the last remaining image layer of a file.
Other Options
Search String
You can define or modify the Search string for the image layers to be imported. In the
Perform a Customized Import on page 64
corresponding the drop-down list you can select:
• {search-string} to use the scene string as defined on the Workspace tab.
• {copy of the currently applied search string} will not be updated while the scene string changes. Can be used for further modifications by editing.
• From file to load a file name used to adapt the search string. We recommend using this option. The software automatically detects the proper string based on the information provided by the search string. If the software fails to do so, this is an indication that the search string may be incorrect.
Driver
Keep the default <auto> to automatically select the appropriate image format Driver. If you require a special file format driver you can select it on the drop-down list.
Alias
The image layers are automatically named with numbers, in other words, Layer 1;
Layer 2; Layer 3. Alternatively, you can define aliases for image layers. To do so, you have to initiate all image layers by adding them to the Image Layers list on the Scene tab. Do not forget to assign the correct channel index as follows.
Channel
Display of the Channel number of the image layer as defined by the image file.
No-Data Settings
By default, none is selected, that means no-data areas are not defined. That means all pixels of all values can be analyzed later. If you want to exclude pixels with a specific gray value from a later image analysis, you can set the value of those pixels that are not to be analyzed. Alternatively, you can limit the image analysis to pixels with a specific gray value; they are exclusively used for later image analysis.
1. Set the No-data handling method:
• Select for file to define the same no-data settings for all image layers of the file. Only the no-data settings in the File group are active.
• Select for layer to define no-data settings for each image layers separately.
Only the no-data settings in the Layer groups are active.
2. Set the No-data apply type. Select a method for assignment of no-data areas:
• none: No-data-values are not defined. That means all pixels of all values can be analyzed later.
• and: Select to assign only those overlapping no-data-areas that all image layers have in common. This corresponds to the Intersection check box of the Assign No-Data-Value dialog box.
• or: Select to assign the no-data-areas of all individual layers for the whole scene, that is if a no data value is found in one image layer, this area is treated as no-data-area in all other image layers. This corresponds to the Union check box of the Assign No-Data-Value dialog box.
• and not reverses the meaning of the value: Pixels with the No-data-value are exclusively used for later image analysis. Select to assign pixels of those overlapping no-data-areas that all images have in common to be used
About Layer Aliases on page 54
Assign No-Data-Values on page 437
for image analysis. The other pixels, that are not having the no-data-value in all image layers, are excluded from image analysis.
• or not reverses the meaning of the value: Pixels with the No-data-value are exclusively used for later image analysis. Select to assign all pixels of the no-data-areas found in at least one image layer to be used for image analysis of the whole scene. (That is if a no data value is found in one layer, this area is treated as no-data-area in all other layers.) The other pixels, that are not of the no-data-value in at least one of the image layers, are excluded from image analysis.
3. Edit the No-data-value to a specific gray value:
• For the No-data apply types and and or it defines those pixels to be excluded from later image analysis.
• For the No-data apply types and not and or not it defines those pixels, that are exclusively used for later image analysis.
Thematic Layers Import Options
On the Thematic Layers tab of the Customized Import dialog box, you can configure thematic layers of scenes to be imported. That way, you modify the import template concerning the following options:
• Add and remove thematic layers.
• Define a special search string for thematic layers and attribute files.
• Modify thematic layer aliases.
• Select file format drivers for importing.
• Change the channel index values.
• Modify attribute table column aliases.
• Modify vector file parameters.
Preconditions:
• Define a master file on the Workspace tab. Otherwise, you cannot access the Thematic Layers tab.
• Before modifying the thematic layer options, we recommend that you first test the customized import with the default settings of the Workspace tab.
Perform a Customized Import on page 64
Figure 47: Thematic Layers tab of the Customized Import dialog box.
1. The Thematic Layers tab lists the thematic Layers to be imported with the related Attributes.
2. To add thematic layers click the Add Layer button.
3. To remove a thematic layer, select it and click the Remove Layer button.
Other Options
Geometry search string; Attribute search string
You can define or modify the search strings for the Geometry files containing the thematic layer information to be imported. Further you can define or modify the search strings for the Attribute tables. You need to do this only for special file formats;
common shape file formats such as .dbf and .csv are found automatically. On the corresponding the drop-down list you can select:
• {search-string} to use the scene string as defined on the Workspace tab.
• {copy of the currently applied search string} will not be updated while the scene string changes. Can be used for further modifications by editing.
• From file to load a file name used to adapt the search string. We recommend using this option. The software automatically detects the proper string based on the information provided by the search string. If the software fails to do so, this is an indication that the search string may be incorrect.
Alias
You can define names for thematic layers and then address them later within other projects.
Geometry Driver
Keep the default <auto> to select the appropriate file format Driver automatically. If
About Layer Aliases on page 54
you need a special driver, select it on the drop-down list.
Attribute ID Column
Generally, each attribute table contains a standard column ID containing the IDs for each object. In case you want to set another column as ID, enter it in the text box instead of the default which is ID.
Channel Index
By default, All channels are imported. If you want to load thematic layers which are image files, you may want to choose the image layer that contains the desired thematic information. Just enter the channel index value in the Channel index combo box to import the corresponding image layer, for example, if you enter 2, the second channel in the selected image file is imported.
Attribute table column alias list
In some geographic information systems (GIS) the names of attribute table columns can have only a limited number of characters. In order to display reasonable column names, an attribute table column alias list exists which maps the column aliases to the names.
You can modify attribute table column aliases:
1. Select Add New Aliases and click the ellipsis button. The Enter Column Name dialog box opens.
2. Enter a name of an existing column name. A new item with this name is listed below the Attribute table column alias list group.
3. Select the new item and enter a new column alias.
Vector file parameters
Set parameters for the internal conversion of vector files to raster files:
• Raster line width for line shape files: You can edit the default of 1. Enter a number in pixels, which is used as the width with which a line shall be calculated with.
• Raster point size for point shape files: You can edit the default of 1 defining the pixel size in points.
• Allow diagonal neighborhood for line shape files: If your line shape file is converted into raster elements using 4-neighborhood or 8-neighborhood (diagonal) you can change the setting to Yes.
Metadata Import Options
On the Metadata tab of the Customized Import dialog box, you can load Metadata into the projects to be created and thus modify the import template with regard to the following options:
• Add and remove metadata.
• Define a special search string for metadata files.
• Select format driver to use for importing.
• Set conversions settings to include metadata in the feature tree.
Precondition: Define a master file on the Workspace tab. Otherwise, you cannot access the Metadata tab.
(ellipsis button)
Perform a Customized Import on page 64
Figure 48: Metadata tab of the Customized Import dialog box.
1. The Metadata tab lists the metadata to be imported in groups.
2. To add a metadata group, click the Add Metadata button.
3. To remove a metadata group, select it and click the Remove Metadata button.
Other Options
Name
Edit the name of the metadata group.
Search String
Define the search string for the metadata files. In the corresponding drop-down list you can select:
• {search-string} to use the scene string as defined on the Workspace tab.
• {copy of the currently applied search string} will not be updated while the scene string changes. Can be used for further modifications by editing.
• From file to load a file name used to adapt the search string. We recommend using this option. The software automatically detects the proper string based on the information provided by the search string. If the software fails to do so, this is an indication that the search string may be incorrect.
Driver
If you know the file format driver applicable for your metadata, we recommend that you select it using the drop-down list. Otherwise, keep the default <auto> to automatically select an image format Driver.
Conversion Settings
When importing metadata you have to convert available external metadata to an internal metadata definition. Click the ellipsis button to open the Metadata Conversion dialog box.
Scenes Import Options
On the Scene tab of the Customized Import dialog box, you can configure image layers of scenes to be imported and thus modify the import template with regard to scene properties like geocoding, unit or site settings.
Precondition: Define a master file on the Workspace tab. Without a master file, you cannot access the Metadata tab.
Figure 49: Scene tab of the Customized Import dialog box.
Properties
Use Geocoding
If your image data is geocoded you can make position coordinates available.
Note
Geocoding is a technique relevant to satellite and aerial photography. Commonly it has no relevance for image analysis in life sciences.
In the drop-down list you can select from the following:
• No: Geocoding information or not imported or not existing.
• Yes: Geocoding information is imported.
• Automatic from file: Automatic import depending on the existence of geocoding in the imported file.
(ellipsis button) Convert Metadata to Provide it to the Feature Tree on page 52
Perform a Customized Import on page 64
About Geocoding on page 50
Unit
For feature calculations, value display, and export, you may select another Unit on the corresponding drop-down list.
If you select Auto, the unit is applied according to the included geocoding information.
If there is no geocoding information included the unit is pixel.
Pixel Size
For feature calculations, value display, and export, you can change the Pixels size. If you keep the default Auto, the unit conversion is applied according to unit of the coordinate system of the image data as follows:
• In case of included geocoding information, the pixel size is equal to the resolution.
• In other cases, pixel size is 1 unit of the coordinate system, for example pixel,
•m, or m.
Scene Extent
Define the Scene extent if the loaded image layers have different sizes. On the drop-down list you can select from the following:
• First scene only: All images must have the same size.
• Scene file: The Sample File selected on the Workspace tab determines the extent of the scene. Image layers with larger sizes are cut off at the boundaries of the sample file. Use geocoding if you want to have the single image layers aligned correctly.
• Union: The scene has the maximal extent based on all input image layers.
• Intersection: The extent of the scene is determined by the overlapping area of all input image layers.
Well Information for Plates
Well string
For the customized import of well, you can specify how well coordinates are parsed from well name. You can use {x} and {y} variables for specifying well coordinates or {x0} and {y0) variables for zero-based coordinates.
Examples:
Well Name Well String Using Regular Expressions A - 2 {x} - {y} {x:1}{any:"[^A-Z0-9]*"}{y}
c1r1 c{x}r{y}
Zero-based indexing like c0r2
c{x0}r{y0}
Available only for
Definiens eCognition Life Server
Site Information for Plates
For the customized import of sites, you have to add some site information to the search string.
x-coo; y-coo
Select either Decimal or Hexadecimal numbers for the X-coordinates or Y-coordinates.
Site String
Define the string for the site. Use {x} or {y} variables to identify the site index within scene name. Example: 001_003.tif requires a site string {x}_{y}.tif
Use Scene Index as Site Index
Select Yes for automatic site recognition. Select No if you want to define the X-coordinates and Y-X-coordinates manually.