Development dependencies for web application:
- node v14.15.1 which is the LTS version of the fermium series
I recommend using nvm -- a node package manager to enable the use of different versions of node for different projects: https://github.com/nvm-sh/nvm
Setting up dpendencies on macos:
# install or upgrade nvm
curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.37.2/install.sh | bash
# restart terminal or reload terminal startup script
. ~/.bash_profile
# install latest LTS version of node
nvm install --lts=fermium
# Installing with latest version of LTS line: fermium
# v14.15.1 is already installed.
# Now using node v14.15.1 (npm v6.14.8
Clone or download this repository and open a terminal shell in the directory.
Setup the development environment for this application.
# install npm development packages for this application
npm install
# install the gulp-cli package globally
npm install --global gulp-cli
Use gulp to start the server and reload/compile files that change and reload the browser.
gulp
# [01:24:52] Requiring external module esm
# [01:24:54] Using gulpfile ~/dev/00-clients/rlmg/cfa-own-fits/gulpfile.esm.js
# [01:24:54] Starting 'default'...
# [01:24:54] Starting 'serve'...
# [01:24:54] Finished 'serve' after 12 ms
# [01:24:54] Starting 'watch'...
# [Browsersync] Access URLs:
# --------------------------------------
# Local: http://localhost:3000
# External: http://192.168.1.108:3000#
# --------------------------------------
# UI: http://localhost:3001
# UI External: http://localhost:3001
# --------------------------------------
A chrome browser window will automatically open at address: http://localhost:3000 when the gulp process starts.
The browser will automatically reload the page when changes are saved to the html, javascript, json or css styles file.
The css styles are written in the scss variant of Sass and when changes are saved the css files are generated from the scss files and the browser will reload the page.
https://jestjs.io/docs/en/getting-started.html
Processing FITS images
The python program ./bin/extract.py processes folders of fits files in directories in the ./fits directory and generates corresponding directories in the ./rawdata directory containing binary arrays of float32 values extracted from image ddata in the original fits files.
To run use pip
to install the numpy, matplotlib and fitsio
python packages.
$ python3 -V
Python 3.8.3
$ pip3 install numpy matplotlib fitsio scipy wand
Generate the raw data image files for infrared, xray, and optical M82 fits files.
[cfa-own-fits ruby-2.6.6 (master)]$ ./bin/extract.py fits/M82
using numpy version: 1.19.1
using matplotlib version: 3.3.2
input path exists: fits/M82
dirname: M82
outdir: rawdata/M82
--------
processing: fits/M82/M82_Spitzer_mid_Infrared.FITS
original_filename: M82_Spitzer_mid_Infrared.FITS
base_filename: M82_Spitzer_mid_Infrared
hdus: 1
img datatype: float64
normalizing image with datatype float64 to float32
size: 1612900 (1.54 MB)
x: 1270
y: 1270
percentiles:
percentile 0.001: 0.0
percentile 0.01: 0.0
percentile 0.1: 0.0
percentile 1: 1.01
percentile 5: 1.05
percentile 10: 1.07
percentile 50: 1.2
percentile 90: 3.03
percentile 95: 6.04
percentile 99: 49.59
percentile 99.9: 756.58
percentile 99.99: 2350.04
min: 0.0
max: 3107.1
next min: 0.095
count: less than next min: 9050
next after next min: 0.613
count: less than next min: 9293
Clipping to next_min and percentile 99: 0.095, 49.588
clipped min: 0.095
clipped max: 49.588
Shifting data to 0
shifted min: 0.0
shifted max: 49.492
Rescaling data to 0..10
rescaled min: 0.0
rescaled max: 10.0
Transformed percentiles:
percentile 0.001: 0.0
percentile 0.01: 0.0
percentile 0.1: 0.0
percentile 1: 0.19
percentile 5: 0.19
percentile 10: 0.2
percentile 50: 0.22
percentile 90: 0.59
percentile 95: 1.2
percentile 99: 10.0
percentile 99.9: 10.0
percentile 99.99: 10.0
writing: rawdata/M82/M82_Spitzer_mid_Infrared.bin
--------
processing: fits/M82/M82_Hubble_Optical.FITS
original_filename: M82_Hubble_Optical.FITS
base_filename: M82_Hubble_Optical
hdus: 1
img datatype: float64
normalizing image with datatype float64 to float32
size: 1612900 (1.54 MB)
x: 1270
y: 1270
percentiles:
percentile 0.001: -0.0
percentile 0.01: 0.0
percentile 0.1: 0.0
percentile 1: 0.0
percentile 5: 0.0
percentile 10: 0.0
percentile 50: 1.82
percentile 90: 5.84
percentile 95: 13.1
percentile 99: 48.24
percentile 99.9: 120.43
percentile 99.99: 339.43
min: -11.975
max: 17955.3
next min: 0.0
count: less than next min: 43
next after next min: 0.059
count: less than next min: 670540
min greater than zero: 0.059
count: less than zero: 43
Clipping to `next after next min` and percentile 99.9: 0.059, 48.241
clipped min: 0.059
clipped max: 48.241
Shifting data to 0
shifted min: 0.0
shifted max: 48.182
Rescaling data to 0..10
rescaled min: 0.0
rescaled max: 10.0
Transformed percentiles:
percentile 0.001: 0.0
percentile 0.01: 0.0
percentile 0.1: 0.0
percentile 1: 0.0
percentile 5: 0.0
percentile 10: 0.0
percentile 50: 0.37
percentile 90: 1.2
percentile 95: 2.71
percentile 99: 10.0
percentile 99.9: 10.0
percentile 99.99: 10.0
writing: rawdata/M82/M82_Hubble_Optical.bin
--------
processing: fits/M82/M82_Chandra_Xray_mid_energy.FITS
original_filename: M82_Chandra_Xray_mid_energy.FITS
base_filename: M82_Chandra_Xray_mid_energy
hdus: 1
img datatype: float32
size: 1612900 (1.54 MB)
x: 1270
y: 1270
percentiles:
percentile 0.001: 0.0
percentile 0.01: 0.0
percentile 0.1: 0.0
percentile 1: 0.0
percentile 5: 0.0
percentile 10: 0.0
percentile 50: 0.0
percentile 90: 0.33
percentile 95: 0.67
percentile 99: 4.0
percentile 99.9: 29.67
percentile 99.99: 74.67
min: 0.0
max: 478.3
next min: 0.333
count: less than next min: 1323510
next after next min: 0.667
count: less than next min: 1502082
Clipping to next_min and percentile 99: 0.333, 4.0
clipped min: 0.333
clipped max: 4.0
Shifting data to 0
shifted min: 0.0
shifted max: 3.667
Rescaling data to 0..10
rescaled min: 0.0
rescaled max: 10.0
Transformed percentiles:
percentile 0.001: 0.0
percentile 0.01: 0.0
percentile 0.1: 0.0
percentile 1: 0.0
percentile 5: 0.0
percentile 10: 0.0
percentile 50: 0.0
percentile 90: 0.0
percentile 95: 0.91
percentile 99: 10.0
percentile 99.9: 10.0
percentile 99.99: 10.0
writing: rawdata/M82/M82_Chandra_Xray_mid_energy.bin
Note
Because the raw data in the image in the HST_Lagoon_f656Green.fits has a minimum
value of about -796 I'm setting the minimum displayed value to 0 in the web app.
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