Bug fixes

bug fixes in prep for 0.14.1
jblindsay · Feb 11, 2019 · b1fcc40 · b1fcc40
1 parent 266c939
commit b1fcc40
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Showing 25 changed files with 1,149 additions and 136 deletions.
diff --git a/readme.txt b/readme.txt
@@ -56,13 +56,17 @@ for more details.
 * Release Notes: *
 ******************
 
-Version 0.15.0 (XX-XX-2019)
-
+Version 0.14.1 (10-02-2019)
+- This release largely focuses on bug-fixes rather than feature additions. However, the
+  following tools were added to the library:
+  RasterArea
+
 - Fixed a bug with the MultiscaleTopographicPositionImage tool that prevented proper output
   for files in GeoTIFF format. 
+- Several other tool-specific bug fixes.
 
 Version 0.14.0 (27-01-2019)
-- The release largely focusses on bug-fixes rather than adding new features. The
+- The release largely focuses on bug-fixes rather than adding new features. The
  following tools were added to the project:
     CircularVarianceOfAspect
     EdgeDensity

diff --git a/src/lidar/las.rs b/src/lidar/las.rs
@@ -44,7 +44,7 @@ pub struct LasFile {
     colour_data: Vec<ColourData>,
     waveform_data: Vec<WaveformPacket>,
     pub geokeys: GeoKeys,
-    wkt: String,
+    pub wkt: String,
     // starting_point: usize,
     header_is_set: bool,
     pub use_point_intensity: bool,
@@ -100,6 +100,7 @@ impl LasFile {
         output.file_mode = "w".to_string();
         output.use_point_intensity = true;
         output.use_point_userdata = true;
+        output.wkt = input.wkt.clone();
 
         output.add_header(input.header.clone());
 
@@ -134,9 +135,9 @@ impl LasFile {
         self.header.generating_software = "WhiteboxTools                   ".to_string();
         self.header.number_of_points_by_return_old = [0, 0, 0, 0, 0];
 
-        self.header.x_scale_factor = 0.0001;
-        self.header.y_scale_factor = 0.0001;
-        self.header.z_scale_factor = 0.0001;
+        self.header.x_scale_factor = 0.001;
+        self.header.y_scale_factor = 0.001;
+        self.header.z_scale_factor = 0.001;
 
         self.header_is_set = true;
     }
@@ -1067,7 +1068,7 @@ impl LasFile {
         let mut mantissa: usize = (format!("{}", (self.header.max_x - self.header.min_x).floor()))
             .to_string()
             .len();
-        let mut dec: f64 = 1.0 / 10_f64.powi(8 - mantissa as i32);
+        let mut dec: f64 = 1.0 / 10_f64.powi(7 - mantissa as i32);
         if self.header.x_scale_factor == 0_f64 {
             self.header.x_scale_factor = dec;
         }
@@ -1184,7 +1185,8 @@ impl LasFile {
         for i in 0..(self.header.number_of_vlrs as usize) {
             total_vlr_size += self.vlr_data[i].record_length_after_header as u32;
         }
-        self.header.offset_to_points = 235 + total_vlr_size; // THIS NEEDS TO BE FIXED WHEN LAS 1.4 SUPPORT IS ADDED FOR WRITING
+        // let alignment_bytes = self.header.header_size as u32 + total_vlr_size % 4u32;
+        self.header.offset_to_points = self.header.header_size as u32 + total_vlr_size; // + alignment_bytes; // THIS NEEDS TO BE FIXED WHEN LAS 1.4 SUPPORT IS ADDED FOR WRITING
         u32_bytes = unsafe { mem::transmute(self.header.offset_to_points) };
         writer.write_all(&u32_bytes)?;
 
@@ -1340,6 +1342,18 @@ impl LasFile {
             writer.write_all(&vlr.binary_data)?;
         }
 
+        // ////////////////////
+        // // Alignment bytes /
+        // ////////////////////
+        // if alignment_bytes > 0 {
+        //     println!("alignment bytes: {}", alignment_bytes);
+        //     for a in 0..alignment_bytes {
+        //         writer.write_all(&[0u8]);
+        //     }
+        // }
+
+        // println!("header: {:?}", self.header);
+
         ////////////////////////////////
         // Write the point to the file /
         ////////////////////////////////
@@ -1352,6 +1366,18 @@ impl LasFile {
                     u32_bytes = unsafe { mem::transmute(val) };
                     writer.write_all(&u32_bytes)?;
 
+                    // if i == 0 {
+                    //     println!("first point: {:?}", self.point_data[i]);
+                    // }
+
+                    // if i == 1 {
+                    //     println!("second point: {:?}", self.point_data[i]);
+                    // }
+
+                    // if i == 349527 {
+                    //     println!("last point: {:?}", self.point_data[i]);
+                    // }
+
                     val = ((self.point_data[i].y - self.header.y_offset)
                         / self.header.y_scale_factor) as i32;
                     u32_bytes = unsafe { mem::transmute(val) };
@@ -1369,13 +1395,13 @@ impl LasFile {
 
                     u8_bytes = unsafe { mem::transmute(self.point_data[i].point_bit_field) };
                     writer.write_all(&u8_bytes)?;
-
+                    
                     u8_bytes = unsafe { mem::transmute(self.point_data[i].class_bit_field) };
                     writer.write_all(&u8_bytes)?;
-
+                    
                     u8_bytes = unsafe { mem::transmute(self.point_data[i].scan_angle as i8) };
                     writer.write_all(&u8_bytes)?;
-
+                    
                     if self.use_point_userdata {
                         u8_bytes = unsafe { mem::transmute(self.point_data[i].user_data) };
                         writer.write_all(&u8_bytes)?;

diff --git a/src/raster/arcascii_raster.rs b/src/raster/arcascii_raster.rs
@@ -30,8 +30,14 @@ pub fn read_arcascii(
         }
         if vec[0].to_lowercase().contains("nrows") {
             configs.rows = vec[vec.len() - 1].trim().parse::<f32>().unwrap() as usize;
+            if configs.columns > 0 {
+                data.reserve(configs.rows * configs.columns);
+            }
         } else if vec[0].to_lowercase().contains("ncols") {
             configs.columns = vec[vec.len() - 1].trim().parse::<f32>().unwrap() as usize;
+            if configs.rows > 0 {
+                data.reserve(configs.rows * configs.columns);
+            }
         } else if vec[0].to_lowercase().contains("xllcorner") {
             xllcenter = vec[vec.len() - 1]
                 .trim()

diff --git a/src/raster/arcbinary_raster.rs b/src/raster/arcbinary_raster.rs
@@ -101,6 +101,8 @@ pub fn read_arcbinary(
             yllcenter - (0.5 * configs.resolution_y) + (configs.rows as f64) * configs.resolution_y;
     }
 
+    data.reserve(configs.rows * configs.columns);
+
     // read the data file
     let data_file = file_name.replace(".hdr", ".flt");
     let mut f = File::open(data_file.clone())?;

diff --git a/src/raster/geotiff/mod.rs b/src/raster/geotiff/mod.rs
@@ -296,6 +296,7 @@ pub fn read_geotiff<'a>(
 
     //data = vec![0.0f64; configs.rows * configs.columns];
     data.clear();
+    data.reserve(configs.rows * configs.columns);
     for _ in 0..configs.rows * configs.columns {
         data.push(0.0f64);
     }

diff --git a/src/raster/grass_raster.rs b/src/raster/grass_raster.rs
@@ -25,8 +25,14 @@ pub fn read_grass_raster(
         let vec = line_split.collect::<Vec<&str>>();
         if vec[0].to_lowercase().contains("rows") {
             configs.rows = vec[1].trim().parse::<f32>().unwrap() as usize;
+            if configs.columns > 0 {
+                data.reserve(configs.rows * configs.columns);
+            }
         } else if vec[0].to_lowercase().contains("cols") {
             configs.columns = vec[1].trim().parse::<f32>().unwrap() as usize;
+            if configs.rows > 0 {
+                data.reserve(configs.rows * configs.columns);
+            }
         } else if vec[0].to_lowercase().contains("north") {
             configs.north = vec[1].trim().to_string().parse::<f64>().unwrap();
         } else if vec[0].to_lowercase().contains("south") {

diff --git a/src/raster/idrisi_raster.rs b/src/raster/idrisi_raster.rs
@@ -122,6 +122,8 @@ pub fn read_idrisi(
     configs.resolution_x = (configs.east - configs.west) / configs.columns as f64;
     configs.resolution_y = (configs.north - configs.south) / configs.rows as f64;
 
+    data.reserve(configs.rows * configs.columns);
+
     // read the data file
     let data_file = file_name.replace(".rdc", ".rst");
     let mut f = File::open(data_file.clone())?;

diff --git a/src/raster/mod.rs b/src/raster/mod.rs
@@ -1,8 +1,8 @@
 /*
 This tool is part of the WhiteboxTools geospatial analysis library.
 Authors: Dr. John Lindsay
-Created: June 2, 2017
-Last Modified: 07/12/2018
+Created: 02/06/2017
+Last Modified: 09/02/2019
 License: MIT
 */
 
@@ -250,18 +250,27 @@ impl Raster {
         {
             output.configs.nodata = 1.71041e38;
         }
+        output.data.reserve(output.configs.rows * output.configs.columns);
         output.data = vec![output.configs.nodata; output.configs.rows * output.configs.columns];
         output
     }
 
-    /// Returns the file name of the `Raster`, without the directory.
+    /// Returns the file name of the `Raster`, without the directory and file extension.
     pub fn get_short_filename(&self) -> String {
         let path = Path::new(&self.file_name);
         let file_name = path.file_stem().unwrap();
         let f = file_name.to_str().unwrap();
         f.to_string()
     }
 
+    /// Returns the file extension.
+    pub fn get_file_extension(&self) -> String {
+        let path = Path::new(&self.file_name);
+        let extension = path.extension().unwrap();
+        let e = extension.to_str().unwrap();
+        e.to_string()
+    }
+
     /// Returns the value contained within a grid cell specified
     /// by `row` and `column`.
     pub fn get_value(&self, row: isize, column: isize) -> f64 {

diff --git a/src/raster/saga_raster.rs b/src/raster/saga_raster.rs
@@ -156,6 +156,8 @@ pub fn read_saga(
         row_start = configs.rows - 1;
     }
 
+    data.reserve(configs.rows * configs.columns);
+
     // read the data file
     let data_file = file_name.replace(".sgrd", ".sdat");
     let mut f = File::open(data_file.clone())?;

diff --git a/src/raster/surfer7_raster.rs b/src/raster/surfer7_raster.rs
@@ -120,6 +120,8 @@ pub fn read_surfer7(
     } as usize;
     offset += 4;
 
+    data.reserve(configs.rows * configs.columns);
+
     configs.west = unsafe {
         mem::transmute::<[u8; 8], f64>([
             buffer[offset],

diff --git a/src/raster/surfer_ascii_raster.rs b/src/raster/surfer_ascii_raster.rs
@@ -48,6 +48,7 @@ pub fn read_surfer_ascii_raster(
             }
             configs.columns = vec[0].trim().parse::<f32>().unwrap() as usize;
             configs.rows = vec[1].trim().parse::<f32>().unwrap() as usize;
+            data.reserve(configs.rows * configs.columns);
             row = configs.rows - 1; // files are stored row major, bottom-to-top
             num_cells = configs.rows * configs.columns;
             data.clear();