ASGA Global

Version   0.34.1
Data       10.03.2021
Author    Robert kiewisz
Depends Shiny tidyverse base readxl xlsx zip
License    GPL V3.0

Description Global modules and functions used in ASGA

`Check_Data`

Description

The ASGA test module to check each uploaded data set before analysis. The test module validates if the uploaded data fitting the expected standardized structure.

Usage

<Upload_Data.R>

Check_Data(i) # Check data routine for raw data 
Check_Analysis(File_name) # Check data routine for analyzed data

Arguments


`i`	single-digit number of the uploaded file
`File_name`	name of the uploaded file

Value

Check_Data object create the following components:

Data_frame
`DATA_TEST`	Test output with numeric value interpreted in `Error_Handler` GUI ASGA module
`AnalysisTest`	Test output with numeric value interpreted in `Upload_Data` Global ASGA modules

The ASGA module to handle uploaded files. There are two routines, one for handling raw data set in .xlsx or .am file format. The second one to handle .xlsx files download after analysis by ASGA.

Usage

<server.R>

callModule(Getfiles_Server, "Home")

Value

Upload_Data object creates the following components:

Data_frame
`NUM_FILES`	Constant storing the value of number uploaded data sets
`Amira_df`	Temp file of raw `.am` files
`AMIRA`	Constant value if = TURE the Amira filed are used
`text_dataset`	Variable used in `Error_Handler` GUI ASGA module for displaying messages
`datatype`	Variable used in `Error_Handler` GUI ASGA module for displaying messages
`AnalysisTest`	Test result variable from `Check_Data` Global ASGA modules used to break upload if data are not correct

Details

This module works in tandem with Check_Data, Load_Amira Global ASGA modules and Error_Handler GUI ASGA module

`Load_Amira`

Description

The ASGA module called when the .am file is uploaded by the user. The module is calling three functions (Load_Amira_Nodes, Load_Amira_Points, Load_Amira_Segments) to extract from .am files nodes, points and segments information.

Usage

Load_Amira_Nodes()
Load_Amira_Points()
Load_Amira_Segments()

Example

<Upload_Data.R>

assign(paste("Data", "Node", i, sep = "_"),
              Load_Amira_Nodes(),
              envir = .GlobalEnv
            )

assign(paste("Data", "Points", i, sep = "_"),
              Load_Amira_Points(),
              envir = .GlobalEnv
            )

assign(paste("Data", "Segments", i, sep = "_"),
              Load_Amira_Segments(),
              envir = .GlobalEnv
            )

`Load_Data`

Description

The ASGA module called for each data set before analysis to the standardized spatial graph for analysis.

Usage

<server.R>

callModule(Load_Data, "Home")

Value

Load_Data object create the following components:

Data_frame
`Node`	Data frame containing columns (`Node ID`, `X Coord`, `Y Coord`, `Z Coord`) for each node/MT end
`Points`	Data frame containing columns (`Point ID`, `X Coord`, `Y Coord`, `Z Coord`) for each point in the point cloud
`Segments`	Data frame containing columns (`Segment ID`,`Pole1_00`,... ,`length`, `Node ID #1`, `Node ID #2`, `Point IDs`)
`Segments_1_KMT`	Data frame containing columns (`Segment ID`, `length`, `Node ID #1`, `Node ID #2`, `Point IDs`) for k-fiber in Pole_1
`Segments_2_KMT`	Data frame containing columns (`Segment ID`, `length`, `Node ID #1`, `Node ID #2`, `Point IDs`) for k-fiber in Pole_2
`Segments_KMT`	Data frame containing columns (`Segment ID`, `length`, `Node ID #1`, `Node ID #2`, `Point IDs`) for k-fiber in both poles
`Segments_SMT`	Data frame containing columns (`Segment ID`, `length`, `Node ID #1`, `Node ID #2`, `Point IDs`) for SMTs in Pole_1
`Pole1`	Data frame containing columns (`X`, `Y`, `Z`) for Pole1 coordinates
`Pole2`	Data frame containing columns (`X`, `Y`, `Z`) for Pole2 coordinates

`Save_Data`

Description

The ASGA module called at the end of the analysis to save all indicated data sets.

Example

<Save_Data.R>

  # Save Data for SMT ends -----------------------------------------------------
  tryCatch(
    {
      assign(paste("Data", current_data, "Name", sep = "_"),
             Name_df,
             envir = .GlobalEnv
      )
      write.xlsx(
        get(paste("Data", current_data, "Name", sep = "_")),
        paste("Data/", "Data_", current_data, "_Name.xlsx", sep = "")
      )
    },
    error = function(e) {}
  )

Arguments


`Name`	Name of the file in `.GlobalEnv` to be saved
`Name_df`	Name of the data_frame in `.GlobalEnv`

Details

Only .xlsx are saved if Amira files were used for analysis then also an overwrite by Save_Amira .am files are saved.

`Save_Amira`

Description

The function overwrites the uploaded by user Amira files by supplying additional analysis for visualization in ZiB Amira software.

Usage

Save_amira(x, y, Elements, Data_type)

Arguments


`x`	Data_frame name which should be saved in Amira file
`y`	Data_frame column number which should be saved in Amira file
`Elements`	Type of saved data e.g ("Nodes", "Points", "Segments")
`Data_type`	Type of input e.g. ("int", "float", "float[3]")

Details

Data set that are indicated by the user in x[y] need to be sorted accordingly to the segment number.

Before the .am file is overwrite the x[y] object is checked if the defined element number is the same as in the Amira file.

Example

<Save_Data.R>

tryCatch({
    assign(paste("Amira", "Dataset", current_data, sep = "_"),
        Save_amira(DF, 2, "Segments", "float"),
        envir = .GlobalEnv)
}, error = function(e) {}
)

`Export_Data`

Description

Small unit designed to collect a list of all saved data, zip them and send to download by the user. After the user download data, all files are deleted.

Usage

<server.R>

# to intoduce new formar for downloadHandler
Zip_Files_Format <- list.files(path = getwd(), pattern = Pattern)

Arguments


`Pattern`	Example: ".am$"

Details

Only .xlsx and .am files are collected