Formatting

.gitignore

@@ -157,4 +157,4 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+#.idea/

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.4.1
+  hooks:
+    # Run the linter.
+    # To be renabled once fixes are made.
+    # - id: ruff
+      # args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+        for more information, see https://pre-commit.ci
+    autofix_prs: true
+    autoupdate_branch: ''
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: weekly
+    skip: []
+    submodules: false

INSTALL

@@ -1,7 +1,7 @@
 To install:
 python setup.py build
 and
-python setup.py install 
+python setup.py install
 
 To also install the optional LOFAR features (requires lofar.parmdb + pyrap):
 

README.md

@@ -1,13 +1,13 @@
 # RMextract
-extract TEC, vTEC, Earthmagnetic field and Rotation Measures from GPS and WMM data for radio interferometry observations 
+extract TEC, vTEC, Earthmagnetic field and Rotation Measures from GPS and WMM data for radio interferometry observations
 
 Please cite as: Mevius, M. (2018) RMextract, Astrophysics Source Code Library, record [ascl:1806.024]
 
-WMM model data: 
+WMM model data:
 NCEI Geomagnetic Modeling Team and British Geological Survey. 2019. World Magnetic Model 2020. NOAA National Centers for Environmental Information. doi: 10.25921/11v3-da71, 2020
 
 IRI model:
-D. Bilitza, IRI the International Standard for the Ionosphere, Adv. Radio Sci., 16, 1-11, https://doi.org/10.5194/ars-16-1-2018, 2018. 
+D. Bilitza, IRI the International Standard for the Ionosphere, Adv. Radio Sci., 16, 1-11, https://doi.org/10.5194/ars-16-1-2018, 2018.
 
 IRIPlas model:
 T. Gulyaeva and D. Bilitza, "Towards ISO standard earth ionosphere and plasmasphere model," in New Developments in the Standard Model R. Larsen, Ed. Hauppauge, New York: NOVA, 2012, pp. 1-48.

RMextract/EMM/EMM.py

@@ -10,83 +10,111 @@
 
 
 class WMM:
-    def __init__(self,cof=resource_filename(__name__,'WMM.COF'),date=2010.,lon=0.,lat=0.,h=0.):
+    def __init__(
+        self,
+        cof=resource_filename(__name__, "WMM.COF"),
+        date=2010.0,
+        lon=0.0,
+        lat=0.0,
+        h=0.0,
+    ):
         try:
-            cof=cof.replace("WMM.COF","")
-            if not os.path.isfile(cof+"WMM.COF"):
-                print ("initializing model failed. Did you specify correct location for coefficient files")
+            cof = cof.replace("WMM.COF", "")
+            if not os.path.isfile(cof + "WMM.COF"):
+                print(
+                    "initializing model failed. Did you specify correct location for coefficient files"
+                )
                 return
-            self.WMM_Model=emm.WMM_Model(cof+"WMM",date,lon,lat,h)
+            self.WMM_Model = emm.WMM_Model(cof + "WMM", date, lon, lat, h)
         except (RuntimeError, TypeError, NameError):
-            print ("initializing mdoel failed. Did you specify correct location for coefficient files")
-        self.date=date
-        self.lon=lon
-        self.lat=lat
-        self.h=h
-        self.changed=False
+            print(
+                "initializing mdoel failed. Did you specify correct location for coefficient files"
+            )
+        self.date = date
+        self.lon = lon
+        self.lat = lat
+        self.h = h
+        self.changed = False
 
     def getXYZ(self):
-        '''get BField, convert to (ITRF) X,Y,Z coordinates'''
-        N,E,D=self.getNED()
-        lat=radians(self.lat)
-        lon=radians(self.lon)
-        X=-1*cos(lat)*cos(lon)*D-sin(lat)*cos(lon)*N-sin(lon)*E
-        Y=-1*cos(lat)*sin(lon)*D-sin(lat)*sin(lon)*N+cos(lon)*E
-        Z=-1*sin(lat)*D+N*cos(lat)
-        return X,Y,Z
+        """get BField, convert to (ITRF) X,Y,Z coordinates"""
+        N, E, D = self.getNED()
+        lat = radians(self.lat)
+        lon = radians(self.lon)
+        X = -1 * cos(lat) * cos(lon) * D - sin(lat) * cos(lon) * N - sin(lon) * E
+        Y = -1 * cos(lat) * sin(lon) * D - sin(lat) * sin(lon) * N + cos(lon) * E
+        Z = -1 * sin(lat) * D + N * cos(lat)
+        return X, Y, Z
 
     def getNED(self):
-        #check if something has changed
+        # check if something has changed
         if self.WMM_Model.getDate() != self.date:
-            self.changed=True
+            self.changed = True
             self.WMM_Model.setDate(self.date)
-        if self.WMM_Model.getLon() != self.lon or self.WMM_Model.getLat() != self.lat :
-            self.changed=True
-            self.WMM_Model.setLonLat(self.lon,self.lat)
+        if self.WMM_Model.getLon() != self.lon or self.WMM_Model.getLat() != self.lat:
+            self.changed = True
+            self.WMM_Model.setLonLat(self.lon, self.lat)
         if self.WMM_Model.getHeight() != self.h:
-            self.changed=True
+            self.changed = True
             self.WMM_Model.setHeight(self.h)
         if self.changed:
             self.WMM_Model.setEM()
-            self.changed=False
-
-        return self.WMM_Model.getX(),self.WMM_Model.getY(),self.WMM_Model.getZ()
-        #North, East,Down
-
-    def getProjectedField(self,lon,lat):
-        '''get fieldstrength  in direction lon,lat'''
-        x,y,z=self.getXYZ()
-        return sin(lat)*z+cos(lat)*cos(lon)*x +cos(lat)*sin(lon)*y
+            self.changed = False
 
-    def getProjectedFieldVector(self,lon,lat):
-        '''get field  with one axis projected in direction lon,lat'''
-        x,y,z=self.getXYZ()
-        return [sin(lat)*z+cos(lat)*cos(lon)*x +cos(lat)*sin(lon)*y,
-                -1*sin(lon)*x +cos(lon)*y,
-                cos(lat)*z-sin(lat)*cos(lon)*x -sin(lat)*sin(lon)*y]
+        return self.WMM_Model.getX(), self.WMM_Model.getY(), self.WMM_Model.getZ()
+        # North, East,Down
 
-    def getProjectedFieldArray(self,lon_array,lat_array,h_array,los_dir):
-        '''returns numpy array with projected BField along LOS (given in lon,lat) for ray tracing'''
-        result=np.zeros((len(lon_array),3))
-
-        for idx,self.lon,self.lat,self.h in zip(range(len(lon_array)),lon_array,lat_array,h_array):
-            result[idx]=self.getProjectedFieldVector(los_dir[0],los_dir[1])
+    def getProjectedField(self, lon, lat):
+        """get fieldstrength  in direction lon,lat"""
+        x, y, z = self.getXYZ()
+        return sin(lat) * z + cos(lat) * cos(lon) * x + cos(lat) * sin(lon) * y
+
+    def getProjectedFieldVector(self, lon, lat):
+        """get field  with one axis projected in direction lon,lat"""
+        x, y, z = self.getXYZ()
+        return [
+            sin(lat) * z + cos(lat) * cos(lon) * x + cos(lat) * sin(lon) * y,
+            -1 * sin(lon) * x + cos(lon) * y,
+            cos(lat) * z - sin(lat) * cos(lon) * x - sin(lat) * sin(lon) * y,
+        ]
+
+    def getProjectedFieldArray(self, lon_array, lat_array, h_array, los_dir):
+        """returns numpy array with projected BField along LOS (given in lon,lat) for ray tracing"""
+        result = np.zeros((len(lon_array), 3))
+
+        for idx, self.lon, self.lat, self.h in zip(
+            range(len(lon_array)), lon_array, lat_array, h_array
+        ):
+            result[idx] = self.getProjectedFieldVector(los_dir[0], los_dir[1])
         return result
 
 
 class EMM(WMM):
-    def __init__(self,cof=resource_filename(__name__,'EMM2000.COF'),date=2010.,lon=0.,lat=0.,h=0.):
+    def __init__(
+        self,
+        cof=resource_filename(__name__, "EMM2000.COF"),
+        date=2010.0,
+        lon=0.0,
+        lat=0.0,
+        h=0.0,
+    ):
         try:
-            cof=cof.replace("EMM2000.COF","")
-            if not os.path.isfile(cof+"EMM2000.COF"):
-                print ("initializing model",cof+"EMM2000.COF","failed. Did you specify correct location for coefficient files")
+            cof = cof.replace("EMM2000.COF", "")
+            if not os.path.isfile(cof + "EMM2000.COF"):
+                print(
+                    "initializing model",
+                    cof + "EMM2000.COF",
+                    "failed. Did you specify correct location for coefficient files",
+                )
                 return
-            
-            self.WMM_Model=emm.EMM_Model(cof+"EMM",date,lon,lat,h)
+
+            self.WMM_Model = emm.EMM_Model(cof + "EMM", date, lon, lat, h)
         except (RuntimeError, TypeError, NameError):
-            print ("initializing mdoel failed. Did you specify correct location for coefficient files")
-        self.date=date
-        self.lon=lon
-        self.lat=lat
-        self.h=h
-        self.changed=False
+            print(
+                "initializing mdoel failed. Did you specify correct location for coefficient files"
+            )
+        self.date = date
+        self.lon = lon
+        self.lat = lat
+        self.h = h
+        self.changed = False

RMextract/EMM/EMM2006.COF

@@ -133,4 +133,4 @@
  15 12   -0.0122   -0.3175
  15 13   -0.1348    0.2017
  15 14    0.1178    0.0045
- 15 15   -0.1924   -0.0323
+ 15 15   -0.1924   -0.0323

RMextract/EMM/EMM2007.COF

@@ -133,4 +133,4 @@
  15 12   -0.0258   -0.3018
  15 13   -0.1043    0.1802
  15 14    0.1248    0.0019
- 15 15   -0.2030   -0.0546
+ 15 15   -0.2030   -0.0546

RMextract/EMM/EMM2008.COF

@@ -133,4 +133,4 @@
  15 12   -0.0319   -0.2968
  15 13   -0.0867    0.1659
  15 14    0.1288   -0.0080
- 15 15   -0.2127   -0.0613
+ 15 15   -0.2127   -0.0613

RMextract/EMM/EMM2009.COF

@@ -133,4 +133,4 @@
  15 12   -0.0357   -0.2965
  15 13   -0.0793    0.1511
  15 14    0.1344   -0.0122
- 15 15   -0.2360   -0.0622
+ 15 15   -0.2360   -0.0622

RMextract/EMM/EMM_Model.cc

@@ -9,31 +9,31 @@ WMM_Model::~WMM_Model(){
     MAG_FreeMagneticModelMemory(TimedMagneticModel);
     TimedMagneticModel=NULL;
   }
-  for(int i = 0; i < epochs + 1; i++) 
+  for(int i = 0; i < epochs + 1; i++)
     if (MagneticModels[i]){
       MAG_FreeMagneticModelMemory(MagneticModels[i]);
       MagneticModels[i]=NULL;
     }
 };
 
-WMM_Model::WMM_Model(){  
+WMM_Model::WMM_Model(){
   TimedMagneticModel=NULL;
-  
-  for(int i = 0; i < epochs + 1; i++) 
+
+  for(int i = 0; i < epochs + 1; i++)
       MagneticModels[i]=NULL;
 };
 
 WMM_Model::WMM_Model(const char CoeffFile[256], const float date,const float lon,const float lat,const float h){
   TimedMagneticModel=NULL;
-  
-  for(int i = 0; i < epochs + 1; i++) 
+
+  for(int i = 0; i < epochs + 1; i++)
       MagneticModels[i]=NULL;
-    
+
   char filename[256];
   char filenameSV[256];
-  
+
   sprintf(filename, "%s.COF", CoeffFile);
-  
+
   FILE * filename_valid=fopen (filename, "r");
   assert(filename_valid);
   fclose(filename_valid);
@@ -65,13 +65,13 @@ void WMM_Model::setEM()
 
 void WMM_Model::setDate(const float date){
     UserDate.DecimalYear=date; //decimal year
-    
+
 }
 
 void WMM_Model::setLonLat(const float lon,const float lat){
   CoordGeodetic.phi=lat;//lattitude in degrees
   CoordGeodetic.lambda=lon; //longitude in degrees
-    
+
 }
 void WMM_Model::setHeight(const float h){
     CoordGeodetic.HeightAboveEllipsoid=h; //Height above WGS-84 elipsoid
@@ -93,16 +93,16 @@ float WMM_Model::getZ(){
 
 EMM_Model::EMM_Model(const char CoeffFile[256], const float date,const float lon,const float lat,const float h){
   TimedMagneticModel=NULL;
-  
-  for(int i = 0; i < epochs + 1; i++) 
+
+  for(int i = 0; i < epochs + 1; i++)
       MagneticModels[i]=NULL;
   char filename[256];
   char filenameSV[256];
-  
+
   sprintf(filename, "%s%d.COF", CoeffFile,2010);
   sprintf(filenameSV, "%s%dSV.COF",CoeffFile,2010);
   //check if filename exists
-  
+
   FILE * filename_valid=fopen (filename, "r");
   assert(filename_valid);
   fclose(filename_valid);
@@ -133,7 +133,7 @@ EMM_Model::EMM_Model(const char CoeffFile[256], const float date,const float lon
   nMax = MagneticModels[epochs]->nMax;
   NumTerms = ((nMax + 1) * (nMax + 2) / 2);
   TimedMagneticModel = MAG_AllocateModelMemory(NumTerms); /* For storing the time modified WMM Model parameters */
-  for(int i = 0; i < epochs; i++) 
+  for(int i = 0; i < epochs; i++)
     if(MagneticModels[i] == NULL || TimedMagneticModel == NULL)
       {
 	MAG_Error(2);

RMextract/EMM/EMM_Model.h

@@ -15,7 +15,7 @@ extern "C"{
 /* The Geomagnetism Library is used to make a command prompt program. The program prompts
 the user to enter a location, performs the computations and prints the results to the
 standard output. The program expects the files GeomagnetismLibrary.c, GeomagnetismHeader.h,
-EMM2010.COF, EMM2010SV.COF and EGM9615.h to be in the same directory. 
+EMM2010.COF, EMM2010SV.COF and EGM9615.h to be in the same directory.
 
 Manoj.C.Nair
 Nov 23, 2009