Merge branch 'develop' into 'master'

Clean header

Closes #20, #15, #13, #1, and #2

See merge request sdc/grisinv!3

.gitignore

 **/*.pyc
+*.ipynb
 tests/__pycache__ 

README.md

@@ -9,11 +9,11 @@ This is an implementation of VFISV code to facilitate a seamless processing of t
 
 ## Requirements
 
-It is highly recommended to install the pipeline in a new `conda` environment.
-
-If you don't have `conda` installed, check [Miniconda](https://docs.conda.io/en/latest/miniconda.html) for a minimal installer for conda.<br>
+It is highly recommended to install the pipeline in a new `conda` environment. <br>
 
+If you don't have conda installed, check [Miniconda](https://docs.conda.io/en/latest/miniconda.html)  for a minimal installer for conda.<br>
 To install Miniconda:
+
 ```sh
 wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
 bash Miniconda3-latest-Linux-x86_64.sh
@@ -25,11 +25,10 @@ We recommend, you use the conda-forge channel for installing the required packag
 > Note: In the conda-forge channel, NumPy is built against a dummy “BLAS” package. <br> When a user installs NumPy from conda-forge, that BLAS package then gets  <br> installed together with the actual library - this defaults to OpenBLAS ... <br> (see [Numpy Documentation](https://numpy.org/install/) for more info.)
 
 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 and update the LD_LIBRARY_PATH so that the MPI libraries provided by conda takes precedence.
+Next, activate the newly created conda environment.
 ```sh
 conda create -n gris_env -c conda-forge mpi4py numpy scipy gfortran_linux-64 lapack
 conda activate gris_env
-export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
 ```
 
 ## Installation
@@ -39,7 +38,7 @@ pip install git+https://gitlab.leibniz-kis.de/sdc/grisinv.git
 ```
 or clone the repo and run setup
 ```sh
-git clone https://gitlab.leibniz-kis.de/sdc/grisinv
+git clone https://gitlab.leibniz-kis.de/sdc/grisinv.git
 cd grisinv
 python setup.py install
 ```
@@ -66,8 +65,6 @@ Options:
   -n, --numproc INTEGER  Number of processors to run on
   -l, --line FLOAT       Wavelength of the line (Angstrom)
   -w, --width FLOAT      Wavelength range +/- (Angstrom)
-  --mgram TEXT           Output Magnetogram fits file
-  --dgram TEXT           Output Dopplergram fits file
   -h, --help             Show this message and exit.
 ```
 
@@ -76,6 +73,11 @@ Options:
 
 ### Command line utility
 
+First, set the `LD_LIBRARY_PATH` so that the MPI libraries provided by conda takes precedence.
+```shell
+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
 and set the `--numproc` to the required number of processors to run the inversion on.
 
@@ -86,7 +88,7 @@ mpiexec -n 1 vfisv \
   --line=15648.514 \
   --numproc=20 \
   --width=1.8 \
-  --out='Magnetogram.fits'
+  --out='output.fits'
 ```
 or, call `mpiexec` directly with the required number of processors and the python core will distribute the inversion.
 
@@ -96,32 +98,26 @@ mpiexec -n 20 vfisv \
   --id=3 \
   --line=15648.514 \
   --width=1.8 \
-  --out='Magnetogram.fits'
-```
-
-To output both a Magnetogram and Dopplergram, use,
-
-```sh
-mpiexec -n 20 vfisv \
-  --path='/dat/sdc/gris/20150919/level1_split/' \
-  --id=3 \
-  --line=15648.514 \
-  --width=1.8 \
-  --mgram='Magnetogram.fits' \
-  --dgram='Dopplergram.fits'
+  --out='output.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.
 
-```sh
-mpiexec -n 1 python
-```
-
-In python:
+With `example.py`:
 ```python
 from grisinv import vfisv
-inv,header = vfisv('/dat/sdc/gris/20150920/level1_split/',5,15648.514,1.8,20)
+inv, header = vfisv('/dat/sdc/gris/20150920/level1_split/',5,15648.514,1.8,20)
 ```
+you can run,
+```sh
+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 
+```

grisinv/data_files/contact_info.txt

+This Fits-File is a level2 GRIS data file. All header values are
+compliant to the SOLARNET recommedations Version 1.4a found at:
+http://sdc.uio.no/open/solarnet/
+
+Additional information for GRIS can be found at:
+https://doi.org/10.1002/asna.201211738
+Additional information for the GREGOR telescope can be found at:
+https://doi.org/10.1002/asna.201211725
+Additional information about the VFISV code can be found at:
+https://doi.org/10.1007/s11207-010-9515-6
+All data published and curated by the Leibniz Institute for Solar
+Physics (KIS) (http://www.leibniz-kis.de) can be found at:
+http://sdc.leibniz-kis.de

grisinv/data_files/header_list.csv

 Observation Information,POINT_ID,OBSERVER,OBS_TRGT,IOBS,NMAPS,NSTEPS
+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
-Projection and Pointing,PC1_1,PC1_2,PC2_1,PC2_2,AZIMUT,ELEV_ANG,SLITORIE,SOLAR_L0,SOLAR_P0
+L2 Processing,LEVEL,FILENAME,EXTNAME,BTYPE,BUNIT,WAVELNTH,WAVE_STR,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
 Provenance,HISTORY
\ No newline at end of file

grisinv/data_files/line_names.csv

-Fe I,15648.514,15648.510,3.0
\ No newline at end of file
+Fe I,15648.514,15648.510,3.0
+Si I,10827.091,10827.089,1.5
+Ca I,10838.970,10838.970,1.5
\ No newline at end of file

grisinv/vfisv_src/makefile

 # Makefile for VFISV inversion code for double Fabry Perot data
 #-------------------------------------------
 # JM Borrero: Jan 20, 2020
-FC=mpif90
+FC=$(CONDA_PREFIX)/bin/mpif90
 F90F = -c -Ofast -std=legacy #-fcheck=all -g  -Wall
 F77F1 = -c -Ofast -std=legacy #-fcheck=all -g -Wall
 F77F2 = -c -Ofast -std=legacy #-fcheck=all -g -Wall
 
-# For Itchy at KIS
-#LIBS = -L /usr/lib64 -llapack
+#Pipeline under conda
 LIBS = -L $CONDA_PREFIX/lib -llapack
-#LIBS = -L /usr/lib64 -lcfitsio -L /home/vigeesh/conda/envs/mpi_test/lib -llapack
-#LIBS = -L /usr/lib -lcfitsio -L /usr/lib/x86_64-linux-gnu -llapack
-# For Personal Laptop
-#LIBS = -L /opt/mpich/lib -lmpi -L /opt/lapack-3.9.0 -llapack -lrefblas -L /usr/lib -lcfitsio
 
 OBJ = 	hold.o \
 	time_param.o \

setup.py

@@ -62,7 +62,7 @@ setup(
     url=URL,
     license=LICENSE,
     packages=find_packages(),
-    package_data={"grisinv": ["data_files/*.csv"]},
+    package_data={"grisinv": ["data_files/*.*"]},
     include_package_data=True,
     install_requires=install_requires,
     scripts=['versioneer.py'],