Merge pull request #87 from kateharborne/dev-noise

dev-noise
kateharborne · Jun 20, 2023 · 3bf98ef · 3bf98ef
2 parents d3e0675 + 5651c1e
commit 3bf98ef
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Showing 4 changed files with 12 additions and 10 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SimSpin
 Type: Package
 Title: SimSpin - A package for the kinematic analysis of galaxy simulations
-Version: 2.4.9
+Version: 2.4.10
 Author: Katherine Harborne
 Co-author: Alice Serene
 Maintainer: <katherine.harborne@icrar.org>

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,6 @@
-# SimSpin v2.4.8 News
+# SimSpin v2.4.10 News
 
-### Last edit: 13/06/23
+### Last edit: 15/06/23
 
 Below is a table containing a summary of all changes made to SimSpin, since the date this file was created on 26/08/2021.
 
@@ -16,7 +16,8 @@ All changes are noted in the changelog table below.
 
 | Date     	| Summary of change                                                                                                                                                                                                                                                                                                                                                                                                        	| Version 	| Commit                                   	| Author            |
 |----------	|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	|---------	|------------------------------------------	| ----------------- |
-| 13/06/23 | Adding the thermal dispersion component to the observed gas maps. | 2.4.9 | | Kate Harborne |
+| 15/06/23 | Updating the noise implementation for `build_datacube` using the median flux pixel to scale the level of noise such that the S/N does not go extreme towards the peak flux or minimum flux in the image. | 2.4.10 | | Kate Harborne |
+| 13/06/23 | Adding the thermal dispersion component to the observed gas maps. | 2.4.9 | d3e0675a80a0036da3e372344e40bf979ad9ffa7 | Kate Harborne |
 | 09/06/23 | Fixing the SFR maps produced in method = `gas` or `sf gas` mode. Previous values returned were mass-weighted mean SFR along the line-of-sight, now adjusted to give the sum of spawned fraction SFR along the LOS. | 2.4.8 | e1a6dd49d0aa74510c27aba5ccfeac8ab8a5e920 | Kate Harborne | 
 | 26/04/23 | Inverse variance cubes have large values that do not save to FITS successfully. Dividing by 1e40 to remove this issue and incorporating this with the units. Also modifying S/N description to give the MINIMUM S/N in the image, not the maximum. | 2.4.7 | fb904cd302cc6b8edda2032bb68fa8cd6b233f8a | Kate Harborne |
 | 23/04/23 | Fixing the noise implementation in methods spectral and velocity. Adding inverse variance cubes to the output when a S/N value is specified. Incorporating tests to check proper incorporation and behaviour. | 2.4.6 | 8eef4e6dea8f9901b83ced8f2b43cee1438fe034 | Kate Harborne |

diff --git a/R/build_datacube.R b/R/build_datacube.R
@@ -304,8 +304,9 @@ build_datacube = function(simspin_file, telescope, observing_strategy,
       output$variance_cube = noise_cube # initialising empty arrays
 
       noise_cube = .add_noise(output$spectral_cube,
-                              sqrt(min(raw_images$flux_image[raw_images$flux_image > 0], na.rm=T))/
+                              sqrt(median(raw_images$flux_image[raw_images$particle_image > 0], na.rm=T))/
                                 (observation$signal_to_noise*sqrt(raw_images$flux_image)))
+
       output$spectral_cube = output$spectral_cube + noise_cube
       output$variance_cube = 1/(noise_cube)^2
       output$variance_cube[is.infinite(output$variance_cube)] = 0
@@ -369,7 +370,7 @@ build_datacube = function(simspin_file, telescope, observing_strategy,
       output$variance_cube = noise_cube # initialising empty arrays
 
       noise_cube = .add_noise(output$velocity_cube,
-                              sqrt(min(raw_images$flux_image[raw_images$flux_image > 0], na.rm=T))/
+                              sqrt(median(raw_images$flux_image[raw_images$particle_image > 0], na.rm=T))/
                                 (observation$signal_to_noise*sqrt(raw_images$flux_image)))
       noise_image = output$observed_images$flux_image*(rowSums(noise_cube, dims=2)/rowSums(output$velocity_cube, dims=2))
 
@@ -476,7 +477,7 @@ build_datacube = function(simspin_file, telescope, observing_strategy,
       output$variance_cube = noise_cube # initialising empty arrays
 
       noise_cube = .add_noise(output$velocity_cube,
-                              sqrt(min(raw_images$mass_image[raw_images$mass_image > 0], na.rm=T))/
+                              sqrt(median(raw_images$mass_image[raw_images$particle_image > 0], na.rm=T))/
                                 (observation$signal_to_noise*sqrt(raw_images$mass_image)))
       noise_image = output$observed_images$flux_image*(rowSums(noise_cube, dims=2)/rowSums(output$velocity_cube, dims=2))
 

diff --git a/tests/testthat/test_utilities.R b/tests/testthat/test_utilities.R
@@ -123,7 +123,7 @@ test_that("interp_quick fails if given more than a scalar", {
 })
 
 test_that("kernel weights sum to 1", {
-  expect_true(sum(.generate_uniform_sphere(100, kernel = "WC2")$weight) == 1)
-  expect_true(sum(.generate_uniform_sphere(100, kernel = "WC6")$weight) == 1)
-  expect_true(sum(.generate_uniform_sphere(100, kernel = "M4")$weight) == 1)
+  expect_equal(sum(.generate_uniform_sphere(100, kernel = "WC2")$weight), 1)
+  expect_equal(sum(.generate_uniform_sphere(100, kernel = "WC6")$weight), 1)
+  expect_equal(sum(.generate_uniform_sphere(100, kernel = "M4")$weight), 1)
 })