Merge pull request #66 from WEgeophysics/master

add exception when reading Tipper data

README.md

@@ -1,25 +1,20 @@
 # _pycsamt_: A package for audio-frequency magnetotellurics
 
-[![Documentation Status](https://readthedocs.org/projects/pycsamt/badge/?version=latest)](https://pycsamt.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/WEgeophysics/pyCSAMT.svg?branch=master)](https://travis-ci.com/WEgeophysics/pyCSAMT) [![Requirements Status](https://requires.io/github/WEgeophysics/pycsamt/requirements.svg?branch=master)](https://requires.io/github/WEgeophysics/pycsamt/requirements/?branch=master)
+[![Documentation Status](https://readthedocs.org/projects/pycsamt/badge/?version=latest)](https://pycsamt.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/WEgeophysics/pyCSAMT.svg?branch=master)](https://travis-ci.com/WEgeophysics/pyCSAMT) 
   ![GitHub](https://img.shields.io/github/license/WEgeophysics/pycsamt?color=blue&label=licence&logo=GNU&logoColor=red) ![GitHub release (latest by date)](https://img.shields.io/github/v/release/WEgeophysics/pyCSAMT?color=orange) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5674430.svg)](https://doi.org/10.5281/zenodo.5674430)
   [![PyPI version](https://badge.fury.io/py/pycsamt.svg)](https://badge.fury.io/py/pycsamt)
-  ![GitHub repo size](https://img.shields.io/github/repo-size/WEgeophysics/pycsamt?color=0A4CEE&style=flat-square)
 
 ## Overview 
 
   * **Purpose**
 
     Previously, the software was intended for controlled source audio-frequency magnetotelluric (CSAMT) data processing (hereinafter the suffix CSAMT) and mostly related
-    to the groundwater exploration. The recent development is focused on the audio-magnetotelluric(AMT) methods i.e the frequency above 1Hz. It encompasses the CSAMT, the natural source AMT (NSAMT) and later the radio AMT. Indeed, the AMT methods are used broadly in diverse of exploration problems such as mineral, hydrocarbon,  groundwater resources, as well as the fault-zone mapping above the 1km depth. 
+    to the groundwater exploration. The recent development is focused on the audio-magnetotelluric(AMT) methods. Indeed, the AMT methods are used broadly in diverse of exploration problems such as mineral, hydrocarbon,  groundwater resources, as well as the fault-zone mapping above the 1km depth. 
     _pycsamt_ is designed to bring a piece of solution to the problems encountered by using AMT methods. It contains steps of AMT data processing and deals with [OCCAM2D](https://marineemlab.ucsd.edu/Projects/Occam/index.html) of [DeGroot-Hedlin and Constable, 1990](https://doi.org/10.1190/1.1442303) , 
     the [MT2DInvMatlab](https://doi.org/10.1016/j.cageo.2008.10.010)  of [Lee et al., 2009](https://doi.org/10.1016/j.cageo.2008.10.010) and [ModEM](https://sites.google.com/site/modularem/download) of [Kelbert et al., 2014](https://doi.org/10.1016/j.cageo.2014.01.010)
     for the modeling purpose.
 
-    It also provides processing tools for filtering data and restoring amplitudes at weak frequency (tensor or or scalar values ) in the "dead-dand"  especially for the NSAMT where the natural signals are not under our control and suffer from frequency ranges with little or no signal. Some implemented filters are the trimming moving-average (MA), the fixed dipole-length MA (both proposed by [Zonge International Engineering (Zonge, 2000)]( http://www.zonge.com/legacy/PDF_DatPro/Astatic.pdf )) and the adaptative MA based on idea of [Torres-verdìn and Bostick, 1992](https://doi.org/10.1190/1.2400625). These filters are mostly used for fast removing the static effect especially in electromagnetic-array profiling survey. Some others filters such as "simple" for outliers removal and "PCA" can also be applied upstream for a particular data where the interferences are very strong (e.g. intenses humman activities, power lines, ...). Moreover, the  "Savitzky-Golay" filter is also added to remove high-frequency noise from data since it has the advantage of preserving the original shape and features of the signal better than other types of filtering approaches such as MA techniques (simple, exponential, cumulative, weight). 
-
- * **A specific WE sub-package**
-
-    Besides the processing features, the software implements a special water exploration (WE) sub-package (geology + drilling ) referred  as `geodrill`, entirely dedicated to improve the groundwater exploration techniques. The aim is to reduce the numerous unsucessful drillings mostly occurred due to their wrong locations after AMT geophysical surveys. It consists to minimize the use of supplement methods to AMT which commonly increases the operating budgets to right locate  the drilling thereby reducing the misinterpretation of modeling results(e.g., demarcating the appropriate fracture zones). More details can be found in the **Citations** section. 
+    It also provides processing tools for filtering and processing data( the trimming moving-average (MA), the fixed dipole-length MA ([Zonge International Engineering (Zonge, 2000)]( http://www.zonge.com/legacy/PDF_DatPro/Astatic.pdf )), the adaptative MA ( [Torres-verdìn and Bostick, 1992](https://doi.org/10.1190/1.2400625)). These filters are mostly used for fast removing the static effect especially in electromagnetic-array profiling survey. Some others filters such as "simple" for outliers removal and "PCA" can also be applied upstream for a particular data where the interferences are very strong (e.g. intenses humman activities, power lines, ...). Moreover, the  "Savitzky-Golay" filter is also added to remove high-frequency noise from data since it has the advantage of preserving the original shape and features of the signal better than other types of filtering approaches such as MA techniques (simple, exponential, cumulative, weight). 
 
  * **Note**
 
@@ -29,7 +24,6 @@
 ## Documentation 
 
 * [Installation Guide](https://pycsamt.readthedocs.io/en/latest/installation.html?highlight=installation)
-* [Demo of PS technique](https://pycsamt.readthedocs.io/en/latest/demo.html?highlight=demo) 
 * [API Documentation](https://pycsamt.readthedocs.io/en/latest/)
 * [Home Page](https://github.com/WEgeophysics/pyCSAMT/wiki)
 * [User Guide](https://github.com/WEgeophysics/pyCSAMT/blob/develop/docs/pyCSAMT%20User%20Guide.pdf)
@@ -61,4 +55,4 @@ We use or link some third-party software (beside the usual tool stack: [Numba](h
 1. Department of Geophysics, School of  Info-physics and Geomatics Engineering, [Central South University](https://en.csu.edu.cn/), China. 
 2. Equipe de Recherche Géophysique Appliquée, Laboratoire de Geologie Ressources Minerales et Energetiques, UFR des Sciences de la Terre et des Ressources Minières, [Université Félix Houphouët-Boigny]( https://www.univ-fhb.edu.ci/index.php/ufr-strm/), Cote d'Ivoire.
 
-* Developer: 1, 2- Kouadio Laurent,  <etanoyau@gmail.com> / <lkk@csu.edu.cn>.
+* Developer: 1, 2- Kouadio Laurent,  <etanoyau@gmail.com> / <lkouao@csu.edu.cn>.

paper.bib

@@ -29,21 +29,14 @@ @article{Berdichevskyetal1998
  year={1998},
  pages={585–606} 
  }
- @article{Carlsonetal2005, 
- title={Applications of controlled source and natural source audio-frequency magnetotellurics to groundwater exploration},
- volume={1}, 
- ISBN={9781622760664},
- ISSN={15548015}, 
- DOI={10.4133/1.2923511}, 
- year={2005}, pages={440–450} 
- }
  @article{deGrootetal1990,
  title={{Occam’s inversion to generate smooth, two-dimensional models from magnetotelluric data}},
  volume={55},
  number={12},
  journal={Geophysics},
  author={DeGroot-Hedlin,C and Constable,S.},
  year={1990},
+ DOI={10.1190/1.1442813},
  pages={1613–1624}
  }
  @article{Goldaketal2015, 
@@ -143,6 +136,7 @@ @article{Labsonetal1985
  volume={50}, number={4}, 
  journal={Geophysics}, 
  author={Labson, V . F and Beckert, A and Morrisson, H.F and Conti, U}, 
+ DOI={10.1190/1.1441940},
  year={1985}, pages={656–664} 
  }
  @misc{Mykle1996,
@@ -225,13 +219,15 @@ @article{Wessel1998
  volume={79},
  journal={Eos Trans. Am. Geophys. Union},
  author={Wessel,D.E. and Smith,W.H},
+ DOI={10.1029/98eo00426},
  year={1998},
  pages={579} 
  }
- @article{Weaver2000,
+ @article{Weaveretal2000,
   title={Characterization of the magnetotelluric tensor in terms of its invariants},
   author={John T. Weaver and Aman K Agarwal and Frederick E. M. Lilley},
   journal={Geophysical Journal International},
+  DOI={10.1046/j.1365-246x.2000.00089.x},
   year={2000},
   volume={141},
   pages={321-336}

pycsamt/modeling/occam2d.py

@@ -437,8 +437,7 @@ def parse_block_data(self, datablocks=None):
                               return_counts= True)
         sites.astype('int32')
         freq.astype('int32')
-
-
+
         # get mode and create model array 
         k_=None 
         m_= [int(s) for s in datum]
@@ -450,8 +449,8 @@ def parse_block_data(self, datablocks=None):
                 self.occam_dtype_ =k_
                 self.occam_dtype_value = values
                 break 
-
         cf =False 
+
         if self.occam_dtype_ =='log_te_tm': 
             self.te_appRho =np.zeros((len(freq), len(sites)))
             self.te_phase = np.zeros((len(freq), len(sites)))
@@ -473,7 +472,11 @@ def parse_block_data(self, datablocks=None):
             self.tm_phase = np.zeros((len(freq), len(sites)))
             self.tm_error_appRho = np.zeros((len(freq), len(sites)))
             self.tm_error_phase = np.zeros((len(freq), len(sites))) 
-
+        else: 
+            raise CSex.pyCSAMTError_occam2d(
+                "Three dimensional and Tipper are not implemented yet."
+                " Please use MTpy (https://github.com/MTgeophysics/mtpy.git)"
+                " or ModEM (http://www.coas.oregonstate.edu) instead.")
         # create for each mode id datablocks 
 
         for kk, rowlines in enumerate(self.data): 
@@ -928,9 +931,6 @@ def read_occam2d_modelfile(self, model_fn=None, mesh_fn=None , iter_fn=None):
             print('** {0:<27} {1} {2}'.format('Occam Roughness params', '=',
                                               self.model_roughness))
 
-
-
-
 class Startup(object): 
     """
     Occam startup file  Actually read startup file.
@@ -1561,8 +1561,6 @@ def truncate_response (data , station_data, station_names ):
                     getattr(self, 'resp_{0}_{1}'.format(
                         occ, fwo.lower())).shape))
 
-
-
 class Mesh(object): 
     """
     Read Occam read mesh file