improved Readme, moved warnings to stderr

.goreleaser.yaml

@@ -38,7 +38,8 @@ archives:
       - goos: windows
         format: zip
     files: 
-      - tutorial/**
+      - LICENSE
+      - README.md
 
 changelog:
   sort: asc

LS_Metadata_reader/metadata_parser.go

@@ -509,7 +509,7 @@ func startProgressReporter(progressTracker *ProgressTracker) {
 		progress := float64(completed) / float64(total) * 100
 		fmt.Printf("\rProgress: %.2f%%", progress)
 		if completed >= total {
-			fmt.Printf("\n")
+			fmt.Println("")
 			break
 		}
 		time.Sleep(100 * time.Millisecond)
@@ -561,11 +561,11 @@ func Reader(directory string, zFlag bool, fFlag bool, p3Flag string) ([]byte, er
 		var getmpc map[string]string
 		config, err := configuration.Getconfig()
 		if err != nil {
-			fmt.Println("Warning: No path config available, we suggest using either --epu or the config to provide the path where EPU mirrors the datasets and stores xmls")
+			fmt.Fprintln(os.Stderr, "Warning: No path config available, we suggest using either --epu or the config to provide the path where EPU mirrors the datasets and stores xmls")
 		} else {
 			errun := json.Unmarshal(config, &getmpc)
 			if errun != nil {
-				fmt.Println("Your config was unretrievable, make sure it is set and accessible or use the param flags")
+				fmt.Fprintln(os.Stderr, "Your config was unretrievable, make sure it is set and accessible or use the param flags")
 			}
 			parallel = getmpc["MPCPATH"]
 		}
@@ -576,7 +576,7 @@ func Reader(directory string, zFlag bool, fFlag bool, p3Flag string) ([]byte, er
 	if parallel != "" {
 		dataFolders, err = findDataFolders(parallel+target, dataFolders)
 		if err != nil {
-			fmt.Println("There should be a folder on your instrument control computer with the same name - something went wrong here", err)
+			fmt.Fprintln(os.Stderr, "There should be a folder on your instrument control computer with the same name - something went wrong here", err)
 			return nil, err
 		}
 	}

README.md

@@ -1,11 +1,11 @@
 # LS Metadata extractor
-simple parser for the two common life-science EM metadata output formats, written in go
+simple parser for the two common life-science EM metadata output formats (.xml from EPU and .mdoc from TOMO5 and SerialEM respectively), written in go
 
 ## Usage
 Chose the appropriate binary from the [Releases](https://github.com/SwissOpenEM/LS_Metadata_reader/releases), then:
-LS_reader_Version target_directory
+LS_Metadata_reader target_directory
 
-For testing, try the associated tutorial folder; an example of how the output should look like is provided in the same folder (tutorial_correct.json). For first time use disregard the warnings about config/flags those are for use directly with EPU or the OpenEM Ingestor.
+For testing, try the associated [tutorial](https://github.com/SwissOpenEM/LS_Metadata_reader/tree/main/tutorial) folder; an example of how the output should look like is provided in the same folder (tutorial_correct.json).
 
 ## Comments
 Runs on a directory containing raw files and their instrument written additional information files (.mdoc and .xml respectively), generates a dataset level .json file. In case of usage with EPU pointing to the top level directory is enough, it will search for the data folders and extract the info from there. Using --z you can also obtain a zip file of the xml files associated with your data collection. If you want all the metadata (dataset level, not all individual entries) written out by a given software use the --f flag, otherwise the output will be OSCEM conform. 
@@ -15,7 +15,13 @@ SerialEM properties examples are to be added to the existing properties files of
 **!!! Requires SerialEM 4.2.0 or newer !!!**
 
 ## For running with EPU directly
-Benefits from setting the "MPCPATH" variable in the .config file (set using LS_reader_version --c) to define the path of data acquistisions mirrored on the microscope PC in EPU. Will work regardless if pointed to the xmls/mdocs otherwise.
+Benefits from setting the config (set using LS_Metadata_reader --c), or handing over the three instrument values directly with flags: 
+--cs 
+--gain_flip_rotate
+--epu 
+The --cs (for the CS value of the instrument) and --gain_flip_rotate (for the orientation of the gain_reference relative to actual data) are unfortunately never provided in the metadata, and are both important for processing. It is therefore highly beneficial to set these two.
+As for --epu, EPU writes its metadata files in a different directory than its actual data (TOMO5 also keeps some additional info that is processed by the LS_Metadata_reader there). It generates another set of folders, usually on the microscope controlling computer, that mirror its OffloadData folders in directory structure. Within them it stores some related information, among which are also the metadata xml files. If --epu is defined as a flag or in the config, the LS_Metadata_reader will directly grab those when the user points it at a OffloadData directory. 
+NOTE: This requires you to mount the microscope computer directory for EPU on the machine you are running LS_Metadata_reader on as those are most likely NOT the same. The extractor will work regardless if pointed to the xmls/mdocs directly, this is just for convenience.
 
 ## Schema-Links 
 Output is compatible to OSCEM schemas https://github.com/osc-em/OSCEM_Schemas/

conversion/converter.go

@@ -156,11 +156,14 @@ func Convert(jsonin []byte, content embed.FS, p1Flag string, p2Flag string) ([]b
 	if p1Flag == "" && p2Flag == "" {
 		config, err := configuration.Getconfig()
 		if err != nil {
-			fmt.Println("Warning: config was not set or could not be obtained - make sure the config is set using LS_Metadata_reader --c or you are using the flags")
+			_ = err
+			//could enable the warning below but its not really required
+			//fmt.Fprintln(os.Stderr, "Warning: config was not set or could not be obtained - make sure the config is set using LS_Metadata_reader --c or you are using the flags")
 		} else {
 			errun := json.Unmarshal(config, &fixvalues)
 			if errun != nil {
-				fmt.Printf("%s", "Warning: Config was found but unreadable")
+				_ = errun
+				//fmt.Fprintln(os.Stderr, "Warning: Config was found but unreadable")
 			}
 		}
 	} else {

main.go

@@ -76,6 +76,7 @@ func main() {
 		cut := strings.Split(cwd, string(os.PathSeparator))
 		name := cut[len(cut)-1] + ".json"
 		os.WriteFile(name, output, 0644)
+		fmt.Println()
 		fmt.Println("Extracted data was written to: ", name)
 
 	} else {
@@ -86,6 +87,7 @@ func main() {
 			twd = strings.Join(conc, ".")
 		}
 		os.WriteFile(twd, output, 0644)
-		fmt.Println("Extracted data was written to: ", twd)
+		fmt.Println()
+		fmt.Printf("Extracted data was written to: %s", twd)
 	}
 }