Improve qc context definition and reporting

rinex-cli/.gitignore

@@ -1,2 +1 @@
-product/
-config/
+workspace/

rinex-cli/README.md

@@ -29,7 +29,7 @@ This tool supports gzip compressed files but the file name must be terminated by
 
 ### Analysis and report files
 
-Reports and plots are rendered in HTML in the `rinex/rinex-cli/product` directory.  
+Reports and plots are rendered in HTML in the `rinex/rinex-cli/workspace` directory.  
 Analysis is named after the primary RINEX file.
 
 ## `teqc` operations
@@ -150,7 +150,7 @@ for every operation that did apply (correct command line description).
 `> record analysis` means the analysis is starting at this point.   
 The location of the graphs that were rendered (if any) is given.
 
-[rinex-cli/product](product/) is where all analysis reports
+[rinex-cli/workspace](workspace/) is where all analysis reports
 get generated. It is named after the main RINEX file (`-fp`) which
 allows preserving sessions for different files.
 

rinex-cli/doc/qc.md

@@ -33,11 +33,9 @@ This allows for example Glonass and other NAV context to be correctly defined.
 1. `--fp [FILE]` for the Observation file
 2. `--nav [FILE1] [FILE2]..` : pass NAV contexts
 
-We will generate products in a dedicated folder.  
-
-The current behavior is to use the 
-[product](https://github.com/gwbres/rinex/tree/rinex-cli/product)
-folder to generate QC reports.
+We will generate products the
+[workspace](https://github.com/gwbres/rinex/tree/rinex-cli/workspace)
+folder, that includes QC reports.
 
 Unlike teqc, we do not support BINEX nor SP3 input data/files as of today.
 

rinex-cli/src/analysis/sampling.rs

@@ -1,28 +1,29 @@
-use crate::{plot::PlotContext, Context};
+use crate::plot::PlotContext;
 use itertools::Itertools;
 use plotly::Histogram; //.sorted()
+use rinex::quality::QcContext;
 
 /*
  * Sampling histogram
  */
-pub fn histogram(ctx: &Context, plot_ctx: &mut PlotContext) {
+pub fn histogram(ctx: &QcContext, plot_ctx: &mut PlotContext) {
     plot_ctx.add_cartesian2d_plot("Sampling Histogram", "Count");
     let durations: Vec<_> = ctx
-        .primary_rinex
+        .primary_data()
         .sampling_histogram()
         .sorted()
         .map(|(dt, _)| dt.to_string())
         .collect();
     let populations: Vec<_> = ctx
-        .primary_rinex
+        .primary_data()
         .sampling_histogram()
         .sorted()
         .map(|(_, pop)| pop.to_string())
         .collect();
     let histogram = Histogram::new_xy(durations, populations).name("Sampling Histogram");
     plot_ctx.add_trace(histogram);
 
-    if let Some(ref nav) = ctx.nav_rinex {
+    if let Some(nav) = &ctx.navigation_data() {
         // Run similar analysis on NAV context
         let durations: Vec<_> = nav
             .sampling_histogram()

rinex-cli/src/analysis/sv_epoch.rs

@@ -1,20 +1,18 @@
-use crate::{
-    plot::{build_chart_epoch_axis, generate_markers, PlotContext},
-    Context,
-};
+use crate::plot::{build_chart_epoch_axis, generate_markers, PlotContext};
 use ndarray::Array;
 use plotly::common::{Marker, Mode, Title, Visible};
 use plotly::layout::Axis;
-use rinex::prelude::*;
+use rinex::{prelude::*, quality::QcContext};
 
 /*
  * Sv per epoch analysis
  */
-pub fn sv_epoch(ctx: &Context, plot_ctx: &mut PlotContext) {
+pub fn sv_epoch(ctx: &QcContext, plot_ctx: &mut PlotContext) {
     plot_ctx.add_cartesian2d_plot("Sv per Epoch", "Sv(PRN#)");
     /*
      * plot customization
-     * dy axis: 1.0, since we're plotting PRN# here
+     * We're plotting PRN#, set dy to +/- 1
+     * for nicer rendition
      */
     let plot_item = plot_ctx.plot_item_mut().unwrap();
     let layout = plot_item.layout().clone().y_axis(
@@ -25,19 +23,20 @@ pub fn sv_epoch(ctx: &Context, plot_ctx: &mut PlotContext) {
     );
     plot_item.set_layout(layout);
 
-    // markers/symbols: one per constellation system
-    let constellations: Vec<_> = ctx.primary_rinex.constellation().collect();
+    // Design markers / symbols
+    //   one per constellation system
+    let constellations: Vec<_> = ctx.primary_data().constellation().collect();
     let mut nb_markers = constellations.len();
 
-    if let Some(ref nav) = ctx.nav_rinex {
+    if let Some(ref nav) = ctx.navigation_data() {
         nb_markers += nav.constellation().count();
     }
 
     let markers = generate_markers(nb_markers);
 
-    let data: Vec<_> = ctx.primary_rinex.sv_epoch().collect();
+    let data: Vec<_> = ctx.primary_data().sv_epoch().collect();
 
-    for (sv_index, sv) in ctx.primary_rinex.sv().enumerate() {
+    for (sv_index, sv) in ctx.primary_data().sv().enumerate() {
         let epochs: Vec<Epoch> = data
             .iter()
             .filter_map(|(epoch, ssv)| {
@@ -68,7 +67,7 @@ pub fn sv_epoch(ctx: &Context, plot_ctx: &mut PlotContext) {
         plot_ctx.add_trace(trace);
     }
 
-    if let Some(ref nav) = ctx.nav_rinex {
+    if let Some(nav) = &ctx.navigation_data() {
         let data: Vec<_> = nav.sv_epoch().collect();
         let nav_constell: Vec<_> = nav.constellation().collect();
 

rinex-cli/src/cli.rs

@@ -1,8 +1,7 @@
-use crate::fops::filename;
-use crate::parser::parse_epoch;
 use clap::{Arg, ArgAction, ArgMatches, ColorChoice, Command};
-use log::{error, info, warn};
-use rinex::{prelude::*, quality::QcOpts, Merge};
+use log::{error, info};
+use rinex::{prelude::*, quality::QcOpts};
+use std::path::Path;
 use std::str::FromStr;
 
 pub struct Cli {
@@ -254,19 +253,8 @@ Refer to README"))
         self.matches.get_one::<String>("filepath").unwrap() // mandatory flag
     }
     /// Returns output filepaths
-    pub fn output_path(&self) -> Option<&str> {
-        if let Some(args) = self.matches.get_one::<String>("output") {
-            Some(&args)
-        } else {
-            None
-        }
-    }
-    pub fn mask_filters(&self) -> Vec<&String> {
-        if let Some(filters) = self.matches.get_many::<String>("mask-filter") {
-            filters.collect()
-        } else {
-            Vec::new()
-        }
+    pub fn output_path(&self) -> Option<&String> {
+        self.matches.get_one::<String>("output")
     }
     pub fn preprocessing(&self) -> Vec<&String> {
         if let Some(filters) = self.matches.get_many::<String>("preprocessing") {
@@ -287,16 +275,24 @@ Refer to README"))
     }
     pub fn qc_config(&self) -> QcOpts {
         if let Some(path) = self.qc_config_path() {
-            let s = std::fs::read_to_string(path).expect(&format!("failed to read \"{}\"", path));
-            let opts: QcOpts = serde_json::from_str(&s).expect("faulty qc configuration");
-            opts
+            if let Ok(content) = std::fs::read_to_string(path) {
+                let opts = serde_json::from_str(&content);
+                if let Ok(opts) = opts {
+                    opts
+                } else {
+                    error!("failed to parse parameter file \"{}\"", path);
+                    info!("using default parameters");
+                    QcOpts::default()
+                }
+            } else {
+                error!("failed to read parameter file \"{}\"", path);
+                info!("using default parameters");
+                QcOpts::default()
+            }
         } else {
             QcOpts::default()
         }
     }
-    pub fn quality_check_separate(&self) -> bool {
-        self.matches.get_flag("qc-separate")
-    }
     pub fn quality_check_only(&self) -> bool {
         self.matches.get_flag("qc-only")
     }
@@ -390,30 +386,39 @@ Refer to README"))
     pub fn quiet(&self) -> bool {
         self.matches.get_flag("quiet")
     }
-    pub fn tiny_html(&self) -> bool {
-        self.matches.get_flag("tiny-html")
-    }
     pub fn cs_graph(&self) -> bool {
         self.matches.get_flag("cs")
     }
+    /*
+     * Returns possible file path to merge
+     */
+    pub fn merge_path(&self) -> Option<&Path> {
+        self.matches
+            .get_one::<String>("merge")
+            .and_then(|s| Some(Path::new(s)))
+    }
     /// Returns optionnal RINEX file to "merge"
     pub fn to_merge(&self) -> Option<Rinex> {
-        let fp = self.matches.get_one::<String>("merge")?;
-        if let Ok(rnx) = Rinex::from_file(&fp) {
-            Some(rnx)
+        if let Some(path) = self.merge_path() {
+            let path = path.to_str().unwrap();
+            if let Ok(rnx) = Rinex::from_file(path) {
+                Some(rnx)
+            } else {
+                error!("failed to parse \"{}\"", path);
+                None
+            }
         } else {
-            error!("failed to parse \"{}\"", filename(fp));
             None
         }
     }
     /// Returns split operation args
     pub fn split(&self) -> Option<Epoch> {
         if self.matches.contains_id("split") {
-            if let Some(args) = self.matches.get_one::<String>("split") {
-                if let Ok(epoch) = parse_epoch(args) {
+            if let Some(s) = self.matches.get_one::<String>("split") {
+                if let Ok(epoch) = Epoch::from_str(s) {
                     Some(epoch)
                 } else {
-                    panic!("failed to parse [DATETIME]");
+                    panic!("failed to parse [EPOCH]");
                 }
             } else {
                 None
@@ -423,52 +428,11 @@ Refer to README"))
         }
     }
     /// Returns optionnal Nav path, for enhanced capabilities
-    pub fn nav_paths(&self) -> Vec<&String> {
-        if let Some(paths) = self.matches.get_many::<String>("nav") {
-            paths.collect()
-        } else {
-            Vec::new()
-        }
-    }
-    /// Returns optionnal Navigation context
-    pub fn nav_context(&self) -> Option<Rinex> {
-        let mut nav_ctx: Option<Rinex> = None;
-        let paths = self.nav_paths();
-        for path in paths {
-            if let Ok(rnx) = Rinex::from_file(&path) {
-                if let Some(ref mut ctx) = nav_ctx {
-                    let _ = ctx.merge_mut(&rnx);
-                } else {
-                    trace!("(nav) augmentation: \"{}\"", filename(&path));
-                    nav_ctx = Some(rnx);
-                }
-            } else {
-                error!("failed to parse navigation file \"{}\"", filename(&path));
-            }
-        }
-        nav_ctx
-    }
-    fn atx_path(&self) -> Option<&String> {
-        if self.matches.contains_id("atx") {
-            self.matches.get_one::<String>("atx")
-        } else {
-            None
-        }
+    pub fn nav_path(&self) -> Option<&String> {
+        self.matches.get_one::<String>("nav")
     }
-    pub fn atx_context(&self) -> Option<Rinex> {
-        if let Some(path) = self.atx_path() {
-            if let Ok(rnx) = Rinex::from_file(&path) {
-                if rnx.is_antex_rinex() {
-                    info!("--atx context provided");
-                    return Some(rnx);
-                } else {
-                    warn!("--atx should be antenna rinex file");
-                }
-            } else {
-                error!("failed to parse atx file \"{}\"", filename(&path));
-            }
-        }
-        None
+    pub fn atx_path(&self) -> Option<&String> {
+        self.matches.get_one::<String>("atx")
     }
     fn manual_ecef(&self) -> Option<&String> {
         self.matches.get_one::<String>("antenna-ecef")