ndarray fixes

doc/releasing.md

@@ -2,6 +2,7 @@
 
 ## Checklist
 
+- [ ] formatting fixed `cargo fmt -- --emit=files`
 - [ ] pipeline is green
 - [ ] everything has been merged into main
 - [ ] update `RELEASES.md`

examples/preprocess.rs

@@ -0,0 +1,110 @@
+//! BYO Array Example
+//! This example demonstrates how to use the `birli` library to preprocess and write out a UVFITS file
+//! from a set of gpubox files and a metafits file.
+//! It uses the `mwalib` and `marlu` libraries to read in the gpubox files and metafits file.
+//! It then uses the `birli` library to preprocess the data and write out a UVFITS file.
+//!
+//! ```bash
+//! cargo run --example preprocess \
+//!     output.uvfits \
+//!     tests/data/1196175296_mwa_ord/1196175296.metafits \
+//!     tests/data/1196175296_mwa_ord/1196175296_20171201145440_gpubox01_00.fits
+//! ```
+
+use std::path::PathBuf;
+
+use birli::{
+    flag_to_weight_array,
+    flags::get_weight_factor,
+    io::{read_mwalib, write_uvfits},
+    marlu::{
+        constants::{
+            COTTER_MWA_HEIGHT_METRES, COTTER_MWA_LATITUDE_RADIANS, COTTER_MWA_LONGITUDE_RADIANS,
+        },
+        mwalib::CorrelatorContext,
+        LatLngHeight, RADec,
+    },
+    FlagContext, PreprocessContext, VisSelection,
+};
+
+fn main() {
+    let args: Vec<String> = std::env::args().collect();
+    let uvfits_path = PathBuf::from(&args[1]);
+    let metafits_path = PathBuf::from(&args[2]);
+    let gpubox_filenames: Vec<PathBuf> = args[3..].iter().map(PathBuf::from).collect();
+
+    let corr_ctx = CorrelatorContext::new(metafits_path, &gpubox_filenames)
+        .expect("unable to get mwalib context");
+
+    let vis_sel = VisSelection::from_mwalib(&corr_ctx).unwrap();
+
+    let flag_ctx = FlagContext::from_mwalib(&corr_ctx);
+    let fine_chans_per_coarse = corr_ctx.metafits_context.num_corr_fine_chans_per_coarse;
+    let mut flag_array = vis_sel.allocate_flags(fine_chans_per_coarse).unwrap();
+    flag_ctx
+        .set_flags(
+            flag_array.view_mut(),
+            &vis_sel.timestep_range,
+            &vis_sel.coarse_chan_range,
+            &vis_sel.get_ant_pairs(&corr_ctx.metafits_context),
+        )
+        .unwrap();
+    let mut jones_array = vis_sel.allocate_jones(fine_chans_per_coarse).unwrap();
+    read_mwalib(
+        &vis_sel,
+        &corr_ctx,
+        jones_array.view_mut(),
+        flag_array.view_mut(),
+        false,
+    )
+    .unwrap();
+
+    // generate weights
+    let weight_factor = get_weight_factor(&corr_ctx);
+    let mut weight_array = flag_to_weight_array(flag_array.view(), weight_factor);
+
+    let prep_ctx = PreprocessContext {
+        array_pos: LatLngHeight {
+            longitude_rad: COTTER_MWA_LONGITUDE_RADIANS,
+            latitude_rad: COTTER_MWA_LATITUDE_RADIANS,
+            height_metres: COTTER_MWA_HEIGHT_METRES,
+        },
+        phase_centre: RADec::from_mwalib_phase_or_pointing(&corr_ctx.metafits_context),
+        correct_van_vleck: true,
+        correct_cable_lengths: false,
+        correct_digital_gains: false,
+        correct_geometry: false,
+        draw_progress: false,
+        passband_gains: None,
+        calsols: None,
+        #[cfg(feature = "aoflagger")]
+        aoflagger_strategy: None,
+    };
+
+    prep_ctx
+        .preprocess(
+            &corr_ctx,
+            jones_array.view_mut(),
+            weight_array.view_mut(),
+            flag_array.view_mut(),
+            &vis_sel,
+        )
+        .unwrap();
+
+    let (avg_time, avg_freq) = (1, 1);
+
+    write_uvfits(
+        &uvfits_path,
+        &corr_ctx,
+        jones_array.view(),
+        weight_array.view(),
+        &vis_sel.timestep_range,
+        &vis_sel.coarse_chan_range,
+        &vis_sel.baseline_idxs,
+        Some(prep_ctx.array_pos),
+        Some(prep_ctx.phase_centre),
+        avg_time,
+        avg_freq,
+    )
+    .unwrap();
+}

src/cli.rs

@@ -1578,7 +1578,7 @@ impl<'a> BirliContext<'a> {
         };
 
         let args_strings = std::env::args().collect_vec();
-        let cmd_line = shlex::join(args_strings.iter().map(String::as_str));
+        let cmd_line = shlex::try_join(args_strings.iter().map(String::as_str))?;
         let application = format!("{PKG_NAME} {PKG_VERSION}");
         let message = prep_ctx.as_comment();
         let history = History {
@@ -3974,8 +3974,10 @@ mod tests_aoflagger_flagset {
             assert_eq!(left_header.num_rows, right_header.num_rows);
             assert_eq!(left_header.num_rows as usize, num_rows);
 
-            let left_flags = $left_flagset.read_flags().unwrap().into_raw_vec();
-            let right_flags = $right_flagset.read_flags().unwrap().into_raw_vec();
+            let (left_flags, left_flags_offset) = $left_flagset.read_flags().unwrap().into_raw_vec_and_offset();
+            assert_eq!(left_flags_offset.unwrap_or(0), 0);
+            let (right_flags, right_flags_offset) = $right_flagset.read_flags().unwrap().into_raw_vec_and_offset();
+            assert_eq!(right_flags_offset.unwrap_or(0), 0);
             assert_eq!(left_flags.len(), right_flags.len());
             assert_eq!(
                 left_flags.len(),

src/error.rs

@@ -1,6 +1,8 @@
 //! Errors that can occur in Birli
 
 use marlu::{io::error::BadArrayShape, mwalib};
+#[cfg(feature = "cli")]
+use shlex::QuoteError;
 use thiserror::Error;
 
 use crate::{
@@ -73,6 +75,11 @@ pub enum BirliError {
     /// Error derived from [`crate::van_vleck::VanVleckCorrection`]
     VanVleckCorrection(#[from] VanVleckCorrection),
 
+    #[cfg(feature = "cli")]
+    #[error(transparent)]
+    /// Error derived from [`shlex::QuoteError`]
+    QuoteError(#[from] QuoteError),
+
     #[error("You selected dry run")]
     /// enum variant for when a dry run is selected
     DryRun {},