From 760d173e8b96de6a9514d7b926c2172378d042ff Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Fri, 20 Feb 2015 22:31:17 +0100
Subject: [PATCH] Added config.py and changed file saving mechanism
magdata/phasemap: load and save methods now dynamically save with absolute
and relative paths. Relative paths are defined in the config.py file!
---
pyramid/__init__.py | 1 +
pyramid/config.py | 18 ++++++++++++++++
pyramid/magdata.py | 52 ++++++++++++++++++++++++++++++++++++---------
pyramid/phasemap.py | 34 +++++++++++++++++++++++++++--
4 files changed, 93 insertions(+), 12 deletions(-)
create mode 100644 pyramid/config.py
diff --git a/pyramid/__init__.py b/pyramid/__init__.py
index 47aba58..5a4b786 100644
--- a/pyramid/__init__.py
+++ b/pyramid/__init__.py
@@ -57,6 +57,7 @@ from .phasemap import * # analysis:ignore
from .phasemapper import * # analysis:ignore
from .projector import * # analysis:ignore
from .regularisator import * # analysis:ignore
+from .config import * # analysis:ignore
from .version import version as __version__
from .version import hg_revision as __hg_revision__
diff --git a/pyramid/config.py b/pyramid/config.py
new file mode 100644
index 0000000..9f45e1f
--- /dev/null
+++ b/pyramid/config.py
@@ -0,0 +1,18 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Feb 20 10:59:42 2015
+
+@author: Jan
+"""
+
+import os
+
+
+__all__ = ['DIR_PACKAGE', 'DIR_MAGDATA', 'DIR_PHASEMAP']
+
+
+DIR_PACKAGE = os.path.join(os.path.dirname(os.path.realpath(__file__)))
+DIR_MAGDATA = os.path.abspath(os.path.join(DIR_PACKAGE, os.pardir, 'files', 'magdata'))
+DIR_PHASEMAP = os.path.abspath(os.path.join(DIR_PACKAGE, os.pardir, 'files', 'phasemap'))
+
+del os
diff --git a/pyramid/magdata.py b/pyramid/magdata.py
index 02920ee..936e4e5 100644
--- a/pyramid/magdata.py
+++ b/pyramid/magdata.py
@@ -331,7 +331,7 @@ class MagData(object):
else:
self.mag_vec = vector
- def save_to_llg(self, filename='..\output\magdata_output.txt'):
+ def save_to_llg(self, filename='magdata.txt'):
'''Save magnetization data in a file with LLG-format.
Parameters
@@ -344,16 +344,22 @@ class MagData(object):
-------
None
- ''' # TODO: Implement default folder for all mag_data and phasemaps!!!
+ '''
self._log.debug('Calling save_to_llg')
- a = self.a * 1.0E-9 / 1.0E-2 # from nm to cm
+ SCALE = 1.0E-9 / 1.0E-2 # from nm to cm
# Create 3D meshgrid and reshape it and the magnetization into a list where x varies first:
- zz, yy, xx = (np.indices(self.dim)-a/2).reshape(3, -1)
+ zz, yy, xx = self.a * SCALE * (np.indices(self.dim)+0.5).reshape(3, -1)
x_vec, y_vec, z_vec = self.magnitude.reshape(3, -1)
- # Save data to file:
data = np.array([xx, yy, zz, x_vec, y_vec, z_vec]).T
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid import DIR_MAGDATA
+ if not os.path.exists(DIR_MAGDATA):
+ os.makedirs(DIR_MAGDATA)
+ filename = os.path.join(DIR_MAGDATA, filename)
+ # Save data to file:
with open(filename, 'w') as mag_file:
- mag_file.write('LLGFileCreator: %s\n' % filename.replace('.txt', ''))
+ mag_file.write('LLGFileCreator: %s\n' % filename)
mag_file.write(' %d %d %d\n' % (self.dim[2], self.dim[1], self.dim[0]))
mag_file.writelines('\n'.join(' '.join('{:7.6e}'.format(cell)
for cell in row) for row in data))
@@ -375,13 +381,20 @@ class MagData(object):
'''
cls._log.debug('Calling load_from_llg')
SCALE = 1.0E-9 / 1.0E-2 # From cm to nm
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid import DIR_MAGDATA
+ if not os.path.exists(DIR_MAGDATA):
+ os.makedirs(DIR_MAGDATA)
+ filename = os.path.join(DIR_MAGDATA, filename)
+ # Load data from file:
data = np.genfromtxt(filename, skip_header=2)
dim = tuple(np.genfromtxt(filename, dtype=int, skip_header=1, skip_footer=len(data[:, 0])))
a = (data[1, 0] - data[0, 0]) / SCALE
magnitude = data[:, 3:6].T.reshape((3,)+dim)
return MagData(a, magnitude)
- def save_to_netcdf4(self, filename='..\output\magdata_output.nc'):
+ def save_to_netcdf4(self, filename='magdata.nc'):
'''Save magnetization data in a file with NetCDF4-format.
Parameters
@@ -396,6 +409,13 @@ class MagData(object):
'''
self._log.debug('Calling save_to_netcdf4')
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid import DIR_MAGDATA
+ if not os.path.exists(DIR_MAGDATA):
+ os.makedirs(DIR_MAGDATA)
+ filename = os.path.join(DIR_MAGDATA, filename)
+ # Save data to file:
mag_file = netCDF4.Dataset(filename, 'w', format='NETCDF4')
mag_file.a = self.a
mag_file.createDimension('comp', 3) # Number of components
@@ -421,14 +441,21 @@ class MagData(object):
A :class:`~.MagData` object containing the loaded data.
'''
- cls._log.debug('Calling copy')
+ cls._log.debug('Calling load_from_netcdf4')
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid import DIR_MAGDATA
+ if not os.path.exists(DIR_MAGDATA):
+ os.makedirs(DIR_MAGDATA)
+ filename = os.path.join(DIR_MAGDATA, filename)
+ # Load data from file:
mag_file = netCDF4.Dataset(filename, 'r', format='NETCDF4')
a = mag_file.a
magnitude = mag_file.variables['magnitude'][...]
mag_file.close()
return MagData(a, magnitude)
- def save_to_x3d(self, filename='..\..\output\magdata_output.x3d', maximum=1):
+ def save_to_x3d(self, filename='magdata.x3d', maximum=1):
'''Output the magnetization in the .x3d format for the Fraunhofer InstantReality Player.
Parameters
@@ -442,7 +469,6 @@ class MagData(object):
'''
self._log.debug('Calling save_to_x3d')
from lxml import etree
-
dim = self.dim
# Create points and vector components as lists:
zz, yy, xx = (np.indices(dim)-0.5).reshape(3, -1)
@@ -483,6 +509,12 @@ class MagData(object):
value='{} {} {}'.format(*spin_color))
etree.SubElement(spin, 'fieldValue', name='spin_scale',
value='{} {} {}'.format(*spin_scale))
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid import DIR_MAGDATA
+ if not os.path.exists(DIR_MAGDATA):
+ os.makedirs(DIR_MAGDATA)
+ filename = os.path.join(DIR_MAGDATA, filename)
# Write the tree into the file in pretty print format:
tree.write(filename, pretty_print=True)
diff --git a/pyramid/phasemap.py b/pyramid/phasemap.py
index ce5c45a..047c275 100644
--- a/pyramid/phasemap.py
+++ b/pyramid/phasemap.py
@@ -5,6 +5,8 @@
"""This module provides the :class:`~.PhaseMap` class for storing phase map data."""
+import os
+
import numpy as np
from numpy import pi
@@ -215,7 +217,7 @@ class PhaseMap(object):
self._log.debug('Calling __imul__')
return self.__mul__(other)
- def save_to_txt(self, filename='..\output\phasemap_output.txt'):
+ def save_to_txt(self, filename='phasemap.txt'):
'''Save :class:`~.PhaseMap` data in a file with txt-format.
Parameters
@@ -230,6 +232,13 @@ class PhaseMap(object):
'''
self._log.debug('Calling save_to_txt')
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid import DIR_PHASEMAP
+ if not os.path.exists(DIR_PHASEMAP):
+ os.makedirs(DIR_PHASEMAP)
+ filename = os.path.join(DIR_PHASEMAP, filename)
+ # Save data to file:
with open(filename, 'w') as phase_file:
phase_file.write('{}\n'.format(filename.replace('.txt', '')))
phase_file.write('grid spacing = {} nm\n'.format(self.a))
@@ -251,13 +260,20 @@ class PhaseMap(object):
'''
cls._log.debug('Calling load_from_txt')
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid import DIR_PHASEMAP
+ if not os.path.exists(DIR_PHASEMAP):
+ os.makedirs(DIR_PHASEMAP)
+ filename = os.path.join(DIR_PHASEMAP, filename)
+ # Load data from file:
with open(filename, 'r') as phase_file:
phase_file.readline() # Headerline is not used
a = float(phase_file.readline()[15:-4])
phase = np.loadtxt(filename, delimiter='\t', skiprows=2)
return PhaseMap(a, phase)
- def save_to_netcdf4(self, filename='..\output\phasemap_output.nc'):
+ def save_to_netcdf4(self, filename='phasemap.nc'):
'''Save :class:`~.PhaseMap` data in a file with NetCDF4-format.
Parameters
@@ -272,6 +288,13 @@ class PhaseMap(object):
'''
self._log.debug('Calling save_to_netcdf4')
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid import DIR_PHASEMAP
+ if not os.path.exists(DIR_PHASEMAP):
+ os.makedirs(DIR_PHASEMAP)
+ filename = os.path.join(DIR_PHASEMAP, filename)
+ # Save data to file:
phase_file = netCDF4.Dataset(filename, 'w', format='NETCDF4')
phase_file.a = self.a
phase_file.createDimension('v_dim', self.dim_uv[0])
@@ -296,6 +319,13 @@ class PhaseMap(object):
'''
cls._log.debug('Calling load_from_netcdf4')
+ # Construct path if filename isn't already absolute:
+ if not os.path.isabs(filename):
+ from pyramid import DIR_PHASEMAP
+ if not os.path.exists(DIR_PHASEMAP):
+ os.makedirs(DIR_PHASEMAP)
+ filename = os.path.join(DIR_PHASEMAP, filename)
+ # Load data from file:
phase_file = netCDF4.Dataset(filename, 'r', format='NETCDF4')
a = phase_file.a
phase = phase_file.variables['phase'][:]
--
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