Differences

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--- eyes:logics:export [2017/06/08 14:56]
bgraf
+++ eyes:logics:export [2017/06/12 19:02] (current)
jschlie1
@@ Line 1: / Line 1: @@
 ====== Export ======
-Exports the data of interest to a a target path.
+Exports the data of interest to a a target path. Different formats can be chosen.
 ===== Usage =====
 Connecting the export logic to any IO enables the user to export the data in multiple different formats and to different locations.
-===== Example ====
+===== Parameters =====
-Here, a very specific example should be given/described. In the future, this can be supported by screenshots etc.. For the moment, give an example easy enough for the user to understand, but specific enough to elaborate why a given parameter is a good set for this very situation.
-===== File Type =====
 Different file types of the dataset to be exported can be chosen.
 |< 100% 30% >|
 ^ File Type                 ^ Description     ^
-|Autodetect | In case of a given data format (e.g. .mrc or .img) the “autodetect” option can be activated. In any other case, the file type needs to be set. |
+| Autodetect | In case of a given data format (e.g. //.mrc// or //.img//) the “autodetect” option can be activated. In any other case, the file type needs to be set. |
-| Header File | To save storage space this option can be used if only the imagic (.hed) file but not the data file (.img) is needed. |
+| Header File | To save storage space this option can be used if only the imagic (//.hed//) file but not the data file (//.img//) is required. |
 | csv  | The //.csv// format is used to store tabular data into plain text (e.g. Excel). |
-| imagic | The file format was developed based on image science convention. Two files are generated, a header (//.hed//) and an image (//.img//) file. In the header file several image specifications are stored. Two files are generated, a header (//.hed//) and an image (//.img//) file. In the header file several image specifications are stored |
+| imagic | The file format was developed based on image science convention. Two files are generated, a header (//.hed//) and an image (//.img//) file. In the header file several image specifications are stored. Two files are generated, a header (//.hed//) and an image (//.img//) file. In the header file an several image specifications are stored |
+| jpg | The images are exported as standard jpg-image-files. |
 | mrc  | The mrc format is based on the map format used in the CCP4 suite for macromolecular crystallography.Two options for MRC-Compatibility may be defined: imagic (1) or xmipp3.1 (2), where parameters are stored according to the mentioned software conventions. For using in RELION rename a //.mrc// stack into //.mrcs//. |
-| star | The STAR (Self-defining Text Archiving and Retrival) formatis an alternative to the XML format to store different kinds of meta data in a easy-to-read fashion. RELION used the star format for all kind of meta data (model.star; optimiser.star; sampling.star and data.star)Notepad++ can be used to read .star files. |
+| png | The images are exported as standard png-image-files. |
+| star | The STAR (Self-defining Text Archiving and Retrival) format is an alternative to the XML format to store different kinds of meta data in a easy-to-read fashion. RELION used the star format for all kind of meta data (model.star; optimiser.star; sampling.star and data.star). //Notepad++// can be used to read //.star//-files. |
+| tif | The images are exported as 32- or 16-bit tif files. |
+|< 100% 30% >|
+^ Parameters                 ^ Description     ^
+| Count                      | Specify, how many images shall be exported, starting from the image defined by parameters Start. |
+| Imagic version             | Define imagic header annotation version. |
+| 3D                         | If checked, the exported data consists of 3Ds. |
+| Start                      | Define, which shall be the first image to be exported. |
+| Coarse factor              | Define applied coarse factor before export. |
+| Cut values to 16bit        | If check, the exported images will be cut to 16 bit before export. |
+| Interpret as RGB           | Pixel values will be interpreted as colored RGB. |
+| Normalize before export    | Images will be normalized before export. |
+| Width                      | Define width of exported images. |
+| Height                     | Define height of exported images. |
+| Depth                      | Define depth (in z-direction) of exported images. |
+| Header size [byte]         | Define header size in byte. |
+| Trailer size [byte]        | Define trailer size in byte. |
+| Endianess                  | Select, whether a big endian or small endian shall be used. |
+| Data type                  | Select data type for exported data. |
+| Append raw header          | Select, whether the raw header should be appended. |
+| Blockname                  | Define Blockname. |
+| Read header only           | Only the file header will be exported. |
+| Convert type               | Select type of conversion. |
+| Header values csv          | Define list of header values to be exported into csv. |
+| File to export to          | Define destination for file export. |
+| Overwrite files            | If at the export destination a file is already existing, decide whether this file shall be overwritten or not. |
+| Split output               | If selected, each image of a stack of images will be exported into an individual file. |
-===== Concept =====
-When a structure is ready, when intermediate results need to be analyzed in a different software, or when graphs, pictures or something similar need to be handled outside of the cow, an export for all kinds of different file formats is needed, which is implemented in this logic.