From 9c3898bf46b1c1184b0f35c85863cd91f3232849 Mon Sep 17 00:00:00 2001
From: Lionel Sambuc <lionel.sambuc@epfl.ch>
Date: Wed, 15 Jan 2020 15:48:18 +0100
Subject: [PATCH] Adding MeshViewer XYZ format support

---
 src/storage/mod.rs |   1 +
 src/storage/xyz.rs | 117 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 118 insertions(+)
 create mode 100644 src/storage/xyz.rs

diff --git a/src/storage/mod.rs b/src/storage/mod.rs
index bd931a9..82303bc 100644
--- a/src/storage/mod.rs
+++ b/src/storage/mod.rs
@@ -1,3 +1,4 @@
 pub mod bincode;
 pub mod json;
 pub mod model;
+pub mod xyz;
diff --git a/src/storage/xyz.rs b/src/storage/xyz.rs
new file mode 100644
index 0000000..b7286ad
--- /dev/null
+++ b/src/storage/xyz.rs
@@ -0,0 +1,117 @@
+use std::collections::HashMap;
+use std::fs::File;
+use std::io::BufReader;
+use std::io::Error;
+use std::io::ErrorKind;
+use std::io::Read;
+
+use super::bincode::store;
+use super::model::v1::Shape;
+use super::model::v1::SpatialObject;
+use super::model::Properties;
+
+fn convert(string: &str) -> Result<Vec<SpatialObject>, Error> {
+    // Read manually the XYZ file, as this is a simple format.
+    // Read line by line, skip all line we don't know how to parse, for the
+    // remaining ones do:
+    //  * lines starting with '#A' we update the current point ID
+    //  * lines we can parse as triplet fo f64, add a position to the list,
+    //     under the oid key.
+    let mut oids = HashMap::new();
+    let mut oid = None;
+    let mut origin = vec![];
+    for line in string.lines() {
+        let values = line.split_whitespace().collect::<Vec<_>>();
+
+        if values.is_empty() {
+            // Skip empty lines
+            continue;
+        }
+
+        match values[0] {
+            "RGBA" => (),
+            "RGB" => (),
+            "SCALE" => (),
+            _ if values[0].starts_with("#A") => {
+                // Update the oid value.
+                oid = Some(format!("{}", values[0].trim_start_matches("#")));
+                trace!("FOUND OID {:?}", oid);
+            }
+            _ if line.contains("WHS") => {
+                // Store the voxel offset value
+                let t: Vec<_> = values[0]
+                    .split(',')
+                    .filter_map(|s| match s.parse::<f64>() {
+                        Err(_) => None,
+                        Ok(v) => Some(v),
+                    })
+                    .collect();
+
+                if t.len() == 3 && origin.is_empty() {
+                    origin = t;
+                } else {
+                    return Err(Error::new(
+                        ErrorKind::InvalidData,
+                        format!("Invalid WHS origin new {:?}, current {:?}", t, origin),
+                    ));
+                }
+                trace!("ORIGIN FOUND: {:?}", origin);
+            }
+            _ if values.len() == 3 => {
+                // Check we have an oid to register the position under first.
+
+                let x = values[0].parse::<f64>();
+                let y = values[1].parse::<f64>();
+                let z = values[2].parse::<f64>();
+
+                if let (Some(oid), Ok(x), Ok(y), Ok(z)) = (oid.clone(), x, y, z) {
+                    trace!("after (oid, x, y, z) = {:?}", (&oid, &x, &y, &z));
+                    // We need to convert these voxel values into mm-s
+                    let (x, y, z) = (x - origin[0], y - origin[1], z - origin[2]);
+                    let (x, y, z) = (x * 0.039_062_5, y * 0.039_062_5, z * 0.039_062_5);
+
+                    oids.entry(oid)
+                        .or_insert_with(|| vec![])
+                        .push(vec![x, y, z]);
+                }
+            }
+            _ => trace!("line {:?}, values: {:?}", line, values),
+        }
+    }
+
+    // Transform the points into SpatialObjects
+    Ok(oids
+        .drain()
+        .map(|(k, v)| {
+            let properties = Properties {
+                type_name: "Feature".to_string(),
+                id: k,
+            };
+
+            let shapes = v
+                .into_iter()
+                .map(|position| Shape {
+                    type_name: "Point".to_string(),
+                    reference_space: "WHS-Rat-um".to_string(),
+                    vertices: vec![position],
+                })
+                .collect();
+
+            SpatialObject { properties, shapes }
+        })
+        .collect())
+}
+
+pub fn from(name: &str) -> Result<(), Error> {
+    // Convert Reference Space definitions
+    let fn_in = format!("{}.xyz", name);
+    let fn_out = format!("{}.bin", name);
+
+    let mut file_in = BufReader::new(File::open(&fn_in)?);
+    let mut string = String::new();
+    file_in.read_to_string(&mut string)?;
+
+    let v = convert(&string)?;
+
+    store(v, &fn_out)
+}