Merge pull request #2 from cmeessen/dev

Merge current version of dev to master

.gitignore

@@ -2,3 +2,4 @@
 velocityconversion_cmeessen.egg-info
 .vscode
 docs/sphinx/build
+Examples/VsSL2013_*.dat

CHANGELOG

@@ -3,12 +3,30 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## [Unreleased]
+### Added
+- Version number is defined within `VelocityConversion/__init__.py` and is being
+  read when building the documentation.
+- The density for the simple pressure calculation can now be defined by
+  declaring the variable `SimpleRho`.
+- Function `Convert()` for convenience when using VelocityConversion as a Python
+  module.
+
+### Changed
+- Enhanced the documentation.
+
 ## [1.1.0] - 2019-07-16
 ### Added
 - Python 3 support.
 - Support for usage of VelocityConversion as a Python module.
 - This CHANGELOG.
 - Function `DefaultMineralogy()`.
+- Added encoding, copyright and license disclaimers.
+- Added option `-dT` to manually adjust the temperature stepping.
+- Added option `-scaleV` to apply a scaling factor to the input velocities.
+- Added warning if velocities are in km/s instead of m/s.
+- Added LoadArray().
+- Added tests with unittest.
 
 ### Changed
 - The function `CalcPT()` was improved. Instead of manually performing the
@@ -17,21 +35,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
   more performant.
 - Updated README.md.
 - Migrated from pep8 to pycodestyle.
-
-## [unreleased] - 2017-11-15
-### Added
-- Added encoding, copyright and license disclaimers.
-
-## [unreleased] - 2017-10-26
-### Added
-- Added option `-dT` to manually adjust the temperature stepping.
-
-## [unreleased] - 2017-10-05
-### Added
-- Added option `-scaleV` to apply a scaling factor to the input velocities.
-- Added warning if velocities are in km/s instead of m/s.
-
-### Changed
 - Fixed a bug in clearing depth values beyond the stored AK135 values.
 
 ## [1.0.1] - 2017-06-22

Examples/RunAsModule.py

@@ -13,7 +13,7 @@
 to DataRaw, for example:
 
 >> SomeArray = np.zeros([10,4])
->> MC.DataRaw = SomeArray
+>> MC.LoadArray(SomeArray)
 """
 
 # Set Velocity type

Examples/VelocityConversion

@@ -1,4 +1,7 @@
 #!/bin/bash
 set -e
 
-python ../VelocityConversion/__init__.py $@
+# Get the directory of this script
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+python $DIR/../VelocityConversion/__init__.py $@

Makefile

@@ -10,3 +10,6 @@ help:
 pycodestyle:
 	pycodestyle --show-source --show-pep8 --ignore=W503,E226,E241 VelocityConversion/__init__.py
 
+docs:
+	cd docs/sphinx && make html
+

README.md

@@ -50,6 +50,26 @@ repository:
 git clone https://github.com/cmeessen/VelocityConversion.git
 ```
 
+To check whether everything is working run the tests
+
+```bash
+python test.py
+```
+
+If the output looks like this, everything is working fine:
+
+```
+test_vp_AlphaConst (__main__.TestVelocityConversion) ... ok
+test_vs_AlphaConst (__main__.TestVelocityConversion) ... ok
+test_vs_AlphaPT (__main__.TestVelocityConversion) ... ok
+test_vs_AlphaT (__main__.TestVelocityConversion) ... ok
+
+----------------------------------------------------------------------
+Ran 4 tests in 1.633s
+
+OK
+```
+
 ### Usage as command line tool
 
 In order to use the code as command line tool, add the `./Examples` directory

VelocityConversion/__init__.py

@@ -47,6 +47,8 @@
 from warnings import warn
 import __main__
 
+__version__ = '1.1.1-rc1'
+
 
 class MantleConversion:
     """The conversion class
@@ -85,6 +87,7 @@ def __init__(self):
         # Rock properties
         self.Composition = None
         self.XFe = None
+        self.SimpleRho = 3000.  # Density kg/m3 for simple pressure computation
 
         # Initialise mineral database
         self.MinDB = self.LoadMineralProperties()
@@ -242,7 +245,7 @@ def AK135(self, depth, simple=False):
             return Pressure
         else:
             self.SimpleP = True
-            return 3000.*self.g*np.absolute(depth)
+            return self.SimpleRho*self.g*np.absolute(depth)
 
     def Alpha(self, P, T, Mineral, p=4.0):
         """Return the thermal expansion coefficient
@@ -574,6 +577,15 @@ def CalcVRho(self, z, T):
 
         return TableVRho
 
+    def Convert(self):
+        """A convenience function to start the converion.
+
+        Calls :meth:`~.FillTables` and :meth:`~.CalcPT`.
+
+        """
+        self.FillTables()
+        self.CalcPT()
+
     def DefaultMineralogy(self):
         """Assign a default mineralogy.
 
@@ -754,6 +766,35 @@ def LoadAlphaTables(self, FileIn='AlphaDB.csv'):
             i_phase = self.Mineralogy['phase'][i]
             self.AlphaPT[:, :, i] = np.reshape(AlphaTables[i_phase], (nP, nT))
 
+    def LoadArray(self, array):
+        """Load a numpy array as input data
+
+        Load a numpy array of shape `[nrows, 4]`. The columns of the array
+        should be:
+
+            +---+---+-------+---------+
+            | X | Y | Z / m | V / m/s |
+            +---+---+-------+---------+
+
+        Parameters
+        ----------
+        array : numpy.array
+            The data array.
+
+        """
+        if array.shape[1] != 4:
+            msg = "Incorrect numbers of columns in input array."
+            raise ValueError(msg)
+        self.DataRaw = array
+        # Remove rows below maximum depth, defined by self.MaxDepth
+        DelRows = np.where(np.abs(self.DataRaw[:, 2]) >= np.abs(self.MaxDepth))
+        if len(DelRows[0]) > 0:
+            print("> Removing depth values beyond", self.MaxDepth, "m.")
+        self.DataRaw = np.delete(self.DataRaw, DelRows, axis=0)
+        self.Depths = np.unique(self.DataRaw[:, 2])
+        self.DataRaw[:, 3] *= self.scaleV
+        self.__check_vmin__()
+
     def LoadMineralogy(self, FileIn=None):
         """
         Import mineralogy of the mantle rock from an input file and perform
@@ -853,15 +894,7 @@ def LoadFile(self, filename=None):
             self.__raise__(ValueError, "No input file defined!")
         print("Loading input file:", self.FileIn)
         print("> Velocity scale factor is", self.scaleV)
-        self.DataRaw = np.loadtxt(self.FileIn)
-        # Remove rows below maximum depth, defined by self.MaxDepth
-        DelRows = np.where(np.abs(self.DataRaw[:, 2]) >= np.abs(self.MaxDepth))
-        if len(DelRows[0]) > 0:
-            print("> Removing depth values beyond", self.MaxDepth, "m.")
-        self.DataRaw = np.delete(self.DataRaw, DelRows, axis=0)
-        self.Depths = np.unique(self.DataRaw[:, 2])
-        self.DataRaw[:, 3] *= self.scaleV
-        self.__check_vmin__()
+        self.LoadArray(np.loadtxt(self.FileIn))
 
     def ReadArgs(self):
         """
@@ -940,6 +973,8 @@ def SaveFile(self, fileout=None):
         Output_h += "XFe - " + str(self.XFe) + "\n"
         if self.SimpleP:
             Output_h += "Pressure calculation: Simplified\n"
+            Output_h += "Pressure calculation density: " + str(self.SimpleRho)
+            Output_h += " kg/m3\n"
         else:
             Output_h += "Pressure calculation: AK135\n"
         Output_h += "Wave frequency (Omega) / Hz: " + str(self.f) + "\n"