From 6ad5ba5825b97436e1241da9b54cb6731ea9b2fd Mon Sep 17 00:00:00 2001
From: Sylwia Majchrowska <s.majchrowska@neurosys.com>
Date: Sat, 31 Jul 2021 23:09:49 +0200
Subject: [PATCH] fix relative path for Rawdata and position of arguments for
 Crim

---
 gprMax/hash_cmds_multiuse.py    | 14 +++++++-------
 user_libs/DebyeFit/Debye_Fit.py |  8 +++++---
 user_models/Rawdata_test.in     |  2 +-
 3 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/gprMax/hash_cmds_multiuse.py b/gprMax/hash_cmds_multiuse.py
index 1a5d140d..e3835461 100644
--- a/gprMax/hash_cmds_multiuse.py
+++ b/gprMax/hash_cmds_multiuse.py
@@ -217,28 +217,28 @@ def process_multicmds(multicmds):
         for cmdinstance in multicmds[cmdname]:
             tmp = cmdinstance.split()
 
-            if len(tmp) != 9:
+            if len(tmp) != 10:
                 logger.exception("'" + cmdname + ': ' + ' '.join(tmp) + "'" + ' requires at exactly nine parameters')
                 raise ValueError
-            if (tmp[5][0] != '[' and tmp[5][-1] != ']') or (tmp[6][0] != '[' and tmp[6][-1] != ']'):
+            if (tmp[3][0] != '[' and tmp[3][-1] != ']') or (tmp[4][0] != '[' and tmp[4][-1] != ']'):
                 logger.exception("'" + cmdname + ': ' + ' '.join(tmp) + "'" + ' requires list at 6th and 7th position')
                 raise ValueError
-            vol_frac = [float(i) for i in tmp[5].strip('[]').split(',')]
-            material = [float(i) for i in tmp[6].strip('[]').split(',')]
+            vol_frac = [float(i) for i in tmp[3].strip('[]').split(',')]
+            material = [float(i) for i in tmp[4].strip('[]').split(',')]
             if len(material) % 3 != 0:
                 logger.exception("'" + cmdname + ': ' + ' '.join(tmp) + "'" + ' each material requires three parameters: e_inf, de, tau_0')
                 raise ValueError
             materials = [material[n:n+3] for n in range(0, len(material), 3)]
 
             setup = Crim(f_min=float(tmp[0]), f_max=float(tmp[1]), a=float(tmp[2]),
-                         sigma=float(tmp[3]), mu=float(tmp[4]), mu_sigma=float(tmp[5]),
                          volumetric_fractions=vol_frac, materials=materials,
-                         number_of_debye_poles=int(tmp[8], material_name=tmp[9]))
+                         sigma=float(tmp[5]), mu=float(tmp[6]), mu_sigma=float(tmp[7]),
+                         number_of_debye_poles=int(tmp[8]), material_name=tmp[9])
             _, properties = setup.run()
 
             multicmds['#material'].append(properties[0].split(':')[1].strip(' \t\n'))
             multicmds['#add_dispersion_debye'].append(properties[1].split(':')[1].strip(' \t\n'))
-    
+
     cmdname = '#Rawdata'
     if multicmds[cmdname] is not None:
         for cmdinstance in multicmds[cmdname]:
diff --git a/user_libs/DebyeFit/Debye_Fit.py b/user_libs/DebyeFit/Debye_Fit.py
index d3db870a..3522cbc7 100644
--- a/user_libs/DebyeFit/Debye_Fit.py
+++ b/user_libs/DebyeFit/Debye_Fit.py
@@ -20,6 +20,7 @@ import numpy as np
 import os
 from matplotlib import pylab as plt
 import matplotlib.gridspec as gridspec
+from pathlib import Path
 import sys
 import scipy.interpolate
 import warnings
@@ -60,7 +61,7 @@ class Relaxation(object):
                                      optimizer class (Default: empty dict).
     :type optimizer_options: dict, optional, default: empty dict
     """
-    
+
     def __init__(self, sigma, mu, mu_sigma,
                  material_name, f_n=50,
                  number_of_debye_poles=-1,
@@ -178,7 +179,7 @@ class Relaxation(object):
         q = self.calculation()
         # Set the real and the imaginary part of the relaxation function
         self.rl, self.im = q.real, q.imag
-        
+
         if self.number_of_debye_poles == -1:
             print("\n#########",
                   "Try to automaticaly fit number of Debye poles, up to 20!",
@@ -609,12 +610,13 @@ class Rawdata(Relaxation):
                                       optimizer=optimizer,
                                       optimizer_options=optimizer_options)
         self.delimiter = delimiter
-        self.filename = filename
+        self.filename = Path(filename).absolute()
         self.params = {'filename':self.filename}
 
     def check_inputs(self):
         """ Check the validity of the inputs. """
         super(Rawdata, self).check_inputs()
+
         if not os.path.isfile(self.filename):
             sys.exit("File doesn't exists!")
 
diff --git a/user_models/Rawdata_test.in b/user_models/Rawdata_test.in
index 40f50e3e..e06bf366 100644
--- a/user_models/Rawdata_test.in
+++ b/user_models/Rawdata_test.in
@@ -2,6 +2,6 @@
 #dx_dy_dz: 0.004 0.004 0.004
 #time_window: 3000
 
-#Rawdata: ../user_libs/DebyeFit/Test.txt 0.1 1 0.1 3 M4
+#Rawdata: user_libs/DebyeFit/Test.txt 0.1 1 0.1 3 M4
 
 #box: 0 0 0 0.07 0.4 0.004 M4