Merge branch 'develop' into 'master'

Clean version, add diagnose

Closes #28, #29, #25, #27, and #14

See merge request sdc/grisinv!7

.gitlab-ci.yml

@@ -3,7 +3,7 @@
 
 .before_script_linux: &before_script_linux
   - apt-get -qq install -y make
-  - conda create -n gris_inv -c conda-forge mpi4py numpy scipy gfortran_linux-64 lapack
+  - conda create -n gris_inv -c conda-forge mpi4py numpy scipy gfortran_linux-64 lapack matplotlib
   - conda init bash
   - source ~/.bashrc
   - conda activate gris_inv

README.md

@@ -27,7 +27,7 @@ We recommend, you use the conda-forge channel for installing the required packag
 First, create a conda environment (e.g named `gris_env`) and install the required packages from conda-forge. <br>
 Next, activate the newly created conda environment.
 ```sh
-conda create -n gris_env -c conda-forge mpi4py numpy scipy gfortran_linux-64 lapack
+conda create -n gris_env -c conda-forge mpi4py numpy scipy gfortran_linux-64 lapack matplotlib
 conda activate gris_env
 ```
 
@@ -78,7 +78,7 @@ First, set the `LD_LIBRARY_PATH` so that the MPI libraries provided by conda tak
 export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
 ```
 
-To run the VFISIV inversion on multi-processor and output a Magnetogram, you can either call `mpiexec` with one processor
+To run the VFISIV inversion on multi-processor, you can either call `mpiexec` with one processor
 and set the `--numproc` to the required number of processors to run the inversion on.
 
 ```sh
@@ -92,7 +92,7 @@ mpiexec -n 1 vfisv \
 ```
 or, call `mpiexec` directly with the required number of processors and the python core will distribute the inversion.
 
-```sh
+```shell
 mpiexec -n 20 vfisv \
   --path='/dat/sdc/gris/20150919/level1_split/' \
   --id=3 \
@@ -101,6 +101,35 @@ mpiexec -n 20 vfisv \
   --out='output.fits'
 ```
 
+```shell
+mpiexec -n 20 vfisv \
+  --path='/dat/sdc/gris/20150919/level1_split/' \
+  --id=3 \
+  --line=15648.514 \
+  --width=1.8 \
+  --out='output.fits'
+```
+
+To output uncertainities, use the `--errors='<filename_erros.fits>'` option.<br>
+
+If you want to check the line fits, use `--diagnose='<filename_diagnose.fits>'`.<br>
+To account for observations with multiple maps, `filename_diagnose` is appended by the map-number, e.g.
+`filename_diagnose_001.fits`
+
+A run with all the options will look like,
+
+```shell
+mpiexec -n 1 vfisv \
+  --path='/dat/sdc/gris/20150919/level1_split/' \
+  --id=3 --line=15648.514 \
+  --numproc=20 \
+  --width=1.8 \
+  --out='test_inversion.fits' \
+  --preview='test_preview.png'  \
+  --errors='test_errors.fits' \
+  --diagnose='test_diagnose.fits' \
+```
+
 ### Python interface
 
 The pipeline can be also be run within a python script. To do so, you need to call the python using `mpiexec` with one processor.
@@ -108,7 +137,7 @@ The pipeline can be also be run within a python script. To do so, you need to ca
 With `example.py`:
 ```python
 from grisinv import vfisv
-inv, header = vfisv('/dat/sdc/gris/20150920/level1_split/',5,15648.514,1.8,20)
+inversions, fits, header = vfisv('/dat/sdc/gris/20150920/level1_split/',5,15648.514,1.8,20)
 ```
 you can run,
 ```sh
@@ -118,6 +147,23 @@ mpiexec -n 1 python example.py
 
 ### Displaying results
 
+
 ```shell
 ds9 -multiframe -match frame image -lock slice image -lock frame image -single -zoom to fit output.fits 
 ```
+
+or, with python (using `sunpy`)
+```python
+from sunpy.map import Map
+m = Map('output.fits')
+#Fitted continuum
+m[0].peek()
+#Line-of-sight velocity
+m[1].peek()
+#Inclination
+m[2].peek()
+#Azimuth
+m[3].peek()
+#Field Strength
+m[3].peek()
+```

grisinv/data_files/header_list.csv

@@ -3,7 +3,7 @@ Temporal Information,DATE,DATE-OBS,DATE-BEG,DATE-END,DATE-AVG
 Instrument and Processing Info,ORIGIN,OBSRVTRY,TELESCOP,INSTRUME,GRATING,CAMERA,OBSGEO-X,OBSGEO-Y,OBSGEO-Z,AWAVLNTH,AWAVMAX,AWAVMIN,WAVEUNIT
 Detector Readout and Data Scaling,OBS_MODE,IMGSYS,XPOSURE,TEXPOSUR,NSUMEXP
 Adaptive Optics and Derotator,AOSYSTEM,AO_LOCK,AO_NMODE,ATMOS_R0,ROTANGLE,ROTCODE,ROTTRACK
-L2 Processing,LEVEL,FILENAME,EXTNAME,BTYPE,BUNIT,WAVELNTH,WAVE_STR,CREATOR,VERS_SW,PRSTEP1,PRPROC1,PRPARA1
+L2 Processing,LEVEL,FILENAME,EXTNAME,BTYPE,BUNIT,WAVELNTH,WAVE_STR,WAVERPIX,WAVERVAL,WAVEDELT,WAVESYER,CREATOR,VERS_SW,PRSTEP1,PRPROC1,PRPARA1
 Projection and Pointing,WCSNAME,WCSAXES,CTYPE1,CUNIT1,CRPIX1,CRVAL1,CDELT1,CSYER1,CTYPE2,CUNIT2,CRPIX2,CRVAL2,CDELT2,CSYER2,CTYPE3,CUNIT3,CRPIX3,CRVAL3,CDELT3,CSYER3,PC1_1,PC1_2,PC2_1,PC2_2,LONPOLE,LATPOLE,MJDREF,AZIMUT,ELEV_ANG,SLITORIE,SOLAR_L0,SOLAR_P0
 Measurement Parameters,GRATANGL,SLIT_WID,STEPSIZE,STEPANGL,SLITCNTR
 File Integrity,CHECKSUM,DATASUM

grisinv/vfisv_src/vfisv_spec.f90

@@ -227,7 +227,14 @@ PROGRAM VFISV_SPEC
   ENDDO
 
   !Send inverted data to the grandmaster.
-  IF (NTASKS == 1) CALL MPI_SEND(INV,LX*LY*16,MPI_REAL,0,4000,intracomm,IERR)
+  IF (NTASKS == 1) THEN
+      CALL MPI_SEND(INV,LX*LY*16,MPI_REAL,0,4000,intracomm,IERR)
+      CALL MPI_SEND(SIFIT,LX*LY*NUMW,MPI_REAL,0,6660,intracomm,IERR)
+      CALL MPI_SEND(SQFIT,LX*LY*NUMW,MPI_REAL,0,6661,intracomm,IERR)
+      CALL MPI_SEND(SUFIT,LX*LY*NUMW,MPI_REAL,0,6662,intracomm,IERR)
+      CALL MPI_SEND(SVFIT,LX*LY*NUMW,MPI_REAL,0,6663,intracomm,IERR)
+  END IF
+
 
   !
   DEALLOCATE(SI,SQ,SU,SV,INV,ICONT)