Results and Exports

amics will rarely be the "last stop" for analysis, and it includes several ways to extract information from amics into other systems generate a "results file" that contains all results export images or data tables batch export tables and images copy and paste data out of amics exports of raw data for archive results files requires amics 5 1 0 or newer the released version of amics is and can be found at amics 5 1 release notes docid\ se8jyhxszdqfpit7s1ja0 with instruction on the software installation docid\ e1faehd1k20uedqhptzlx page manuals for previous versions of the software can be found at the older amics versions docid\ d2biwe sybowhhdww0anz page results files can be a specially formatted access database ( mre), human readable json ( json), a binary file ( bin) file results files differ from other type of exports in three major ways they may optionally be set up update automatically at the end of reclassification the file continues multiple sets of results in tables they contain all data needed for all calculations, but some calculations are expected to be completed on the client side setup to set a default results file export on the completion of reclassification do the following open default settings expand the section "calculation result export options" select the export format as json, mre, or binary select export folder locations set export options some options only to specific exports see each type below for specifics from version 5 onwards, the process settings will allow users to set where to save the alternative data formats (mdb, json, and bin) the three settings will do the following, depending on the measurement folder pm this folder location will be used to export the alternative data format if the measurement data is present in project manager folder non pm this folder location will be used to export the alternative data format if the measurement data is not present in any of the project manager default path this folder location will be used if neither "folder pm" or "folder non pm" have been set it is possible to use a relative folder (e g \results\\), and amics will use the mre folder location as the base, and place export data in the relative folder note amics will use text after the final "\\" as the file name (i e \results\export = export report bin) access database ( mdb) format the mre format legacy export format used by the community, particularly companies and users that utilized jktech's mla software amics maintains this export format to continue to support users using legacy reporting tools and scripts see mdb results export docid mwxvawdypqiaurld6duf for detailed information on the mre format the following settings may be applied export segments cannot be applied in this format export points cannot be applied in this format export spectra cannot be applied to this format export images cannot be applied in this format quant materials cannot be applied in this format use compression cannot be applied in this format use indentation cannot be applied in this format settings that are not applicable are ignored selecting them will have no impact on the file export the mre format is based on microsoft access this database format is no longer supported by microsoft and we cannot guarantee future compatibility we strongly recommend using/migrating to the json or binary exports human readable ( json) format json is one of the most widely used formats in modern computing the format was invented by douglas crockford and chip morningstar (formally of lucasfilm) with the basic concept of embedding a javascript object inside of an html frame they placed strings into quotations to avoid conflicts with javascript reserved words and functions, and json was formed “one of the key design goals behind json was minimalism my idea was that the less we have to agree on in order to inter operate, the more likely we’re going to be able to inter operate well,” said crockford see this history of the format https //hackernoon com/the history of json and the people that created it the official json specification can be found here https //www json org/jsonhttps //www json org/json en html en html the json results export docid\ yahokjegvm99gkhmbmt9o has been designed to take advantage of json's simplicity and portability it has a limited number of tables included and can be written very fast we also hope this format can meet the first requirements of f a i r data https //www go fair org/fair principles/ as we go on a journey together towards modern data export segments cannot be applied in this format export points adds a table into the file for any materials in the tmq screen with the x y locations and quantification results export spectra cannot be applied to this format export images cannot be applied in this format quant materials will apply the selected material quantification if specified, or the standard quantification if not specified, to a sum spectrum from each material the result is presented in the material table this will include a sample quantified assay using the quantified material data and materialarea percent use compression cannot be applied in this format use indentation adds whitespace to the file improves the human readability of the format and more closely aligns with the principals of json however, it results in a much larger file settings that are not applicable are ignored selecting them will have no impact on the file export binary ( bin) format the binary results export docid\ aonct13cbxvn eqsuxhxy is a highly compressible binary format designed to store all results from amics we have published documentation on this file, allowing systems to be designed around it the binary file sacrifices the simplicity of json for maximum functionality the following settings may be applied export segments includes the segment table in the binary export each segment has an entry and this is an effective archive of the classification table from the export points adds a table into the file for any materials in the tmq screen with the x y locations and quantification results export spectra an archive copy of all spectra in the database export images includes the image layers as tiles in the export quant materials will apply the selected material quantification if specified, or the standard quantification if not specified, to a sum spectrum from each material the result is presented in the material table this will include a sample quantified assay using the quantified material data and materialarea percent use compression exports the file as a zip archive use indentation cannot be applied to this format settings that are not applicable are ignored selecting them will have no impact on the file export exports of images, charts, and data tables single file exports are accessible from the "other tools" tab the sub menu will always be responsive to the main window tab that is open image exports images can be exported from either the image tab docid\ didxhv 9p ewca8szipl4 ( feature grid tab docid\ qca7y27uxl7h9ay llm4q image export has yet to be implemented) images may be exported as png, jpeg, bmp, and tiff when exporting a single image the software will remember the most recent selected format export image will export the full extent of the image of the layer that is selected export screen exports the image extent shown on the screen export legend will export the key or list of materials and colors see image exports docid\ p pcwzdirlkh8jsupzj t for more information, including the export of txt metadata formats to make amics files compatible with other hitachi software and cloud systems lap image tile export requires amics 5 1 0 or newer the released version of amics is and can be found at amics 5 1 release notes docid\ se8jyhxszdqfpit7s1ja0 with instruction on the software installation docid\ e1faehd1k20uedqhptzlx page manuals for previous versions of the software can be found at the older amics versions docid\ d2biwe sybowhhdww0anz page the lap image tiles docid 46wtkg0tt o5rvwkupwnt export provides tiff image tiled at the originally collected resolution the intended use of this export is to form the base layer for the creation of image pyramids in downstream software enable the lap file export in the settings and configurations docid\ hwyar6 exfvz2pw8auh2t and export on the "other tools" ribbon export charts exporting charts docid\ cc9netj rahgutaznfvte requires the chart tab to be active from the "other tools" ribbon select the export for image export the image export option will now export the image of the chart it is also possible to right click and copy the image to the clipboard export tables exporting data tables docid\ m40zzosngmtzksfoy vkd requires the calculation tables tab docid aqtjdzmushqruecjuegl to be active this will activate the "calculation' context ribbon this gives the options to export as excel or an access database the data can also be highlighted in the table and right clicked to have the option to copy to the clipboard the entire table or a selection batch exports requires amics 5 1 0 or newer the released version of amics is and can be found at amics 5 1 release notes docid\ se8jyhxszdqfpit7s1ja0 with instruction on the software installation docid\ e1faehd1k20uedqhptzlx page manuals for previous versions of the software can be found at the older amics versions docid\ d2biwe sybowhhdww0anz page the chart and table exports both require the user to select a calculation from the properties interface panel docid\ umouk5dcxzyxemjn7fosb to export the chart two options have been included to minimize the clicking and exporting required both require the user to select a batch list, allowing them to export from many different experiments the "batch reporting function from the "calculations" tab using the reclassification batch processing docid\ dwt1bfepe67kmz13fqvjm tool on the "processing" ribbon the batch calculations export will export only the data tables into a microsoft excel format the export can be organized by selecting how samples are reported and how data is grouped batch will always utilize the layer settings selected on the initializing instance other exports the sqlite raw file docid\ xvlslrjsj38ulrciswh8a is an archive format that includes all spectra in a database the json raw file docid 12 btxt5282aljawfkxio takes a different approach by giving a pixel by pixel classification dataset in json both files have been replaced by the binary results export docid\ aonct13cbxvn eqsuxhxy in amics 5 1 exporting spectrum docid\ jgf2z4te5dwpssdwvx04o is enabled in either bruker spx export docid 93zpvivq 3jbamgfa0hhz or as msa iso spectra export docid\ cswksedooyk0avwkrq8 n spectra can be exported from the reference tab docid\ zuprkvz35edykn6kcncza tmq tab docid\ bgsw1ofaardq9rc3t1gaa , or from any unknown x ray the tmq tab docid\ bgsw1ofaardq9rc3t1gaa provides several exports including exporting points lists