diff --git a/pyramid/semper.py b/pyramid/semper.py
deleted file mode 100644
index 191e18ca764b6a25e75568d87566c96d6b1dba47..0000000000000000000000000000000000000000
--- a/pyramid/semper.py
+++ /dev/null
@@ -1,483 +0,0 @@
-# -*- coding: utf-8 -*-
-# Copyright 2014 by Forschungszentrum Juelich GmbH
-# Author: J. Caron
-#
-"""This module provides the :class:`~.SemperFormat` class which allows reading and writing `.unf`
-files which are used in Semper."""
-
-
-import os
-from time import strftime
-import numpy as np
-import struct
-
-from pyramid.phasemap import PhaseMap
-from pyramid.magdata import MagData
-
-import logging
-
-
-__all__ = ['SemperFormat']
-
-
-class SemperFormat(object):
-
- '''Class for importing and exporting Semper `.unf`-files.
-
- The :class:`~.SemperFormat` class represents a Semper binary file format with a header, which
- holds additional information. Floating point images can be converted to :class:`~.PhaseMaps',
- complex value images can be converted to :class:`~.MagData'-slices (2D magnetization along
- a simple axis) and vice versa with the corresponding methods and classmethods. `.unf`-files
- can also be saved and read from files.
-
- Attributes
- ----------
- dim : tuple (N=3)
- Dimensions of the data.
- a : float
- Grid spacing (nm per pixel).
- data : :class:`~numpy.ndarray` (N=3)
- The phase map or magnetization information in a 3D array (with one slice).
- iclass : int
- Defines the image class defined in `ICLASS_DICT`. Normally `image` (1) is chosen.
- iform : int
- Defines the data format defined in 'IFORM_DICT'.
- iversn :
- Current `.unf`-format version. Current: 2.
- ilabel : int
- Defines if a label is present (1) or not (0).
- iformat : int
- Defines if the file is formatted (1) or not (0).
- title : string
- Title of the file (not to be confused with the filename).
- iwp : int
- Write protect flag, determining if picture is (1) or is not (0) write-projtected.
- ipltyp : int
- Position type list. Standard seems to be 0 (picture not a position list).
- date : string
- The date of file construction.
- iccoln : int
- Column number of picture origin.
- icrown : int
- Row number of picture origin.
- iclayn : int
- Layer number of picture origin.
-
- '''
-
- _log = logging.getLogger(__name__)
-
- ICLASS_DICT = {1: 'image', 2: 'macro', 3: 'fourier', 4: 'spectrum',
- 5: 'correlation', 6: 'undefined', 7: 'walsh', 8: 'position list',
- 9: 'histogram', 10: 'display look-up table'}
-
- IFORM_DICT = {0: np.byte, 1: np.int32, 2: np.float32, 3: np.complex64}
-
- def __init__(self, arg_dict):
- self._log.debug('Calling __init__')
- self.dim = arg_dict['dim']
- self.a = arg_dict['a']
- self.data = arg_dict['data']
- self.iclass = arg_dict['ICLASS']
- self.iform = arg_dict['IFORM']
- self.iversn = arg_dict['IVERSN']
- self.ilabel = arg_dict['ILABEL']
- self.iformat = arg_dict['IFORMAT']
- self.title = arg_dict['title']
- self.iwp = arg_dict['IWP']
- self.ipltyp = arg_dict['IPLTYP']
- self.date = arg_dict['date']
- self.iccoln = arg_dict['ICCOLN']
- self.icrown = arg_dict['ICROWN']
- self.iclayn = arg_dict['ICLAYN']
- self._log.debug('Created '+str(self))
-
- @classmethod
- def from_file(self, filename):
- '''Load a `.unf`-file into a :class:`~.SemperFormat` object.
-
- Parameters
- ----------
- filename : string
- The name of the unf-file from which to load the data. Standard format is '\*.unf'.
-
- Returns
- -------
- semper : :class:`~.SemperFormat` (N=1)
- Semper file format object containing the loaded information.
-
- '''
- self._log.debug('Calling from_file')
- # Construct path if filename isn't already absolute:
- if not os.path.isabs(filename):
- from pyramid import DIR_FILES
- directory = os.path.join(DIR_FILES, 'semper')
- if not os.path.exists(directory):
- os.makedirs(directory)
- filename = os.path.join(directory, filename)
- with open(filename, 'rb') as f:
- # Read header:
- rec_length = np.frombuffer(f.read(4), dtype=np.int32)[0] # length of header
- header = np.frombuffer(f.read(rec_length), dtype=np.int16)
- ncol, nrow, nlay = header[:3]
- dim = (nlay, nrow, ncol)
- iclass = header[3]
- iform = header[4]
- data_format = self.IFORM_DICT[iform]
- iflag = header[5]
- iversn, remain = divmod(iflag, 10000)
- ilabel, ntitle = divmod(remain, 1000)
- iformat = header[6] if len(header) == 7 else None
- assert np.frombuffer(f.read(4), dtype=np.int32)[0] == rec_length
- # Read title:
- title = ''
- if ntitle > 0:
- assert np.frombuffer(f.read(4), dtype=np.int32)[0] == ntitle # length of title
- title_bytes = np.frombuffer(f.read(ntitle), dtype=np.byte)
- title = ''.join(map(chr, title_bytes))
- assert np.frombuffer(f.read(4), dtype=np.int32)[0] == ntitle
- # Read label:
- iwp, date, range_string, ipltype, a = [None] * 5 # Initialization!
- iccoln, icrown, iclayn = [None] * 3
- if ilabel:
- rec_length = np.frombuffer(f.read(4), dtype=np.int32)[0] # length of label
- label = np.frombuffer(f.read(512), dtype=np.int16)
- assert ''.join([chr(l) for l in label[:6]]) == 'Semper'
- assert struct.unpack('>h', ''.join([chr(x) for x in label[6:8]]))[0] == ncol
- assert struct.unpack('>h', ''.join([chr(x) for x in label[8:10]]))[0] == nrow
- assert struct.unpack('>h', ''.join([chr(x) for x in label[10:12]]))[0] == nlay
- iccoln = struct.unpack('>h', ''.join([chr(x) for x in label[12:14]]))[0]
- icrown = struct.unpack('>h', ''.join([chr(x) for x in label[14:16]]))[0]
- iclayn = struct.unpack('>h', ''.join([chr(x) for x in label[16:18]]))[0]
- assert label[18] == iclass
- assert label[19] == iform
- iwp = label[20]
- date = '{}-{}-{} {}:{}:{}'.format(label[21]+1900, *label[22:27])
- ncrang = label[27]
- assert sum(label[ncrang+28:55]) == 0 # unused bytes
- ipltyp = label[55] # position list type
- real_coords = label[62]
- if real_coords:
- a = struct.unpack('<f', ''.join([chr(x) for x in label[83:87]]))[0]
- assert a == struct.unpack('<f', ''.join([chr(x) for x in label[91:95]]))[0]
- else:
- a = 1
- assert ''.join([str(unichr(l)) for l in label[100:100+ntitle]]) == title
- assert np.frombuffer(f.read(4), dtype=np.int32)[0] == rec_length
- # Read picture data:
- data = np.empty((nlay, nrow, ncol), dtype=data_format)
- for k in range(nlay):
- for j in range(nrow):
- rec_length = np.frombuffer(f.read(4), dtype=np.int32)[0] # length of row
- row = np.frombuffer(f.read(rec_length), dtype=data_format)
- data[k, j, :] = row
- assert np.frombuffer(f.read(4), dtype=np.int32)[0] == rec_length
- arg_dict = {}
- arg_dict['dim'] = dim
- arg_dict['a'] = a
- arg_dict['data'] = data
- arg_dict['ICLASS'] = iclass
- arg_dict['IFORM'] = iform
- arg_dict['IVERSN'] = iversn
- arg_dict['ILABEL'] = ilabel
- arg_dict['IFORMAT'] = iformat
- arg_dict['title'] = title
- arg_dict['IWP'] = iwp
- arg_dict['IPLTYP'] = ipltyp
- arg_dict['date'] = date
- arg_dict['ICCOLN'] = iccoln
- arg_dict['ICROWN'] = icrown
- arg_dict['ICLAYN'] = iclayn
- return SemperFormat(arg_dict)
-
- def to_file(self, filename='semper.unf', skip_header=False):
- '''Save a :class:`~.SemperFormat` to a file.
-
- Parameters
- ----------
- filename : string, optional
- The name of the unf-file to which the data should be written.
- skip_header : boolean, optional
- Determines if the header, title and label should be skipped (useful for some other
- programs). Default is False.
-
- Returns
- -------
- None
-
- '''
- self._log.debug('Calling to_file')
- # Construct path if filename isn't already absolute:
- if not os.path.isabs(filename):
- from pyramid import DIR_FILES
- directory = os.path.join(DIR_FILES, 'semper')
- if not os.path.exists(directory):
- os.makedirs(directory)
- filename = os.path.join(directory, filename)
- nlay, nrow, ncol = self.dim
- with open(filename, 'wb') as f:
- if not skip_header:
- # Create header:
- header = []
- header.extend(reversed(list(self.dim))) # inverse order!
- header.append(self.iclass)
- header.append(self.iform)
- header.append(self.iversn*10000 + self.ilabel*1000 + len(self.title))
- if self.iformat is not None:
- header.append(self.iformat)
- # Write header:
- f.write(struct.pack('I', 2*len(header))) # record length, 4 byte format!
- for element in header:
- f.write(struct.pack('h', element)) # 2 byte format!
- f.write(struct.pack('I', 2*len(header))) # record length!
- # Write title:
- f.write(struct.pack('I', len(self.title))) # record length, 4 byte format!
- f.write(self.title)
- f.write(struct.pack('I', len(self.title))) # record length!
- # Create label:
- if self.ilabel:
- label = np.zeros(256, dtype=np.int32)
- label[:6] = [ord(c) for c in 'Semper']
- label[6:8] = divmod(ncol, 256)
- label[8:10] = divmod(nrow, 256)
- label[10:12] = divmod(nlay, 256)
- label[12:14] = divmod(self.iccoln, 256)
- label[14:16] = divmod(self.icrown, 256)
- label[16:18] = divmod(self.iclayn, 256)
- label[18] = self.iclass
- label[19] = self.iform
- label[20] = self.iwp
- year, time = self.date.split(' ')
- label[21:24] = map(int, year.split('-'))
- label[21] -= 1900
- label[24:27] = map(int, time.split(':'))
- range_string = '{:.4g},{:.4g}'.format(self.data.min(), self.data.max())
- ncrang = len(range_string)
- label[27] = ncrang
- label[28:28+ncrang] = [ord(s) for s in range_string]
- label[55] = self.ipltyp
- label[62] = 1 # Use real coords!
- label[75:79] = [ord(x) for x in struct.pack('<f', self.a)] # RealCoord DZ
- label[79:83] = [ord(x) for x in struct.pack('<f', self.a*self.iclayn)] # Z0
- label[83:87] = [ord(x) for x in struct.pack('<f', self.a)] # RealCoord DY
- label[87:91] = [ord(x) for x in struct.pack('<f', self.a*self.iccoln)] # Y0
- label[91:95] = [ord(x) for x in struct.pack('<f', self.a)] # RealCoord DX
- label[95:99] = [ord(x) for x in struct.pack('<f', self.a*self.icrown)] # X0
- label[100:100+len(self.title)] = [ord(s) for s in self.title]
- label[244:248] = [ord(c) for c in 'nm'] + [0]*2 # x unit
- label[248:252] = [ord(c) for c in 'nm'] + [0]*2 # y unit
- label[252:256] = [ord(c) for c in 'nm'] + [0]*2 # z unit
- # Write label:
- if self.ilabel:
- f.write(struct.pack('I', 2*256)) # record length, 4 byte format!
- for element in label:
- f.write(struct.pack('h', element)) # 2 byte format!
- f.write(struct.pack('I', 2*256)) # record length!
- # Write picture data:
- for k in range(nlay):
- for j in range(nrow):
- row = self.data[k, j, :]
- factor = 8 if self.iform == 3 else 4 # complex numbers need more space!
- f.write(struct.pack('I', factor*ncol)) # record length, 4 byte format!
- if self.iform == 0: # bytes:
- raise Exception('Byte data is not supported! Use int, float or complex!')
- elif self.iform == 1: # int:
- for element in row:
- f.write(struct.pack('i', element)) # 4 bytes per data entry!
- elif self.iform == 2: # float:
- for element in row:
- f.write(struct.pack('f', element)) # 4 bytes per data entry!
- elif self.iform == 3: # complex:
- for element in row:
- f.write(struct.pack('f', element.real)) # 4 bytes per data entry!
- f.write(struct.pack('f', element.imag)) # 4 bytes per data entry!
- f.write(struct.pack('I', factor*ncol)) # record length, 4 byte format!
-
- @classmethod
- def from_phasemap(self, phase_map, title='PYRAMID-PhaseMap'):
- '''Export info from a :class:`~.PhaseMap` object to a :class:`~.SemperFormat` object.
-
- Parameters
- ----------
- phase_map : :class:`~.PhaseMap`
- Phase map object which should be converted.
- title : string, optional
- Title of the file (not to be confused with the filename).
-
- Returns
- -------
- semper : :class:`~.SemperFormat` (N=1)
- Semper file format object containing the loaded information.
-
- '''
- self._log.debug('Calling from_phasemap')
- arg_dict = {}
- arg_dict['dim'] = (1,) + phase_map.dim_uv
- arg_dict['a'] = phase_map.a
- arg_dict['data'] = np.expand_dims(phase_map.phase, axis=0)
- arg_dict['ICLASS'] = 1 # image
- arg_dict['IFORM'] = 2 # float
- arg_dict['IVERSN'] = 2 # current standard
- arg_dict['ILABEL'] = 1 # True
- arg_dict['IFORMAT'] = None # not needed
- arg_dict['title'] = title
- arg_dict['IWP'] = 0 # seems standard
- arg_dict['IPLTYP'] = 248 # seems standard
- arg_dict['date'] = strftime('%y-%m-%d %H:%M:%S')
- arg_dict['ICCOLN'] = phase_map.dim_uv[1]//2 + 1
- arg_dict['ICROWN'] = phase_map.dim_uv[0]//2 + 1
- arg_dict['ICLAYN'] = 1
- return SemperFormat(arg_dict)
-
- def to_phasemap(self):
- '''Export info from a :class:`~.SemperFormat` object to a :class:`~.PhaseMap` object.
-
- Parameters
- ----------
- None
-
- Returns
- -------
- phase_map : :class:`~.PhaseMap`
- The created phase map object.
-
- Notes
- -----
- Only works if the `iform` parameter is `2` (floating point values).
-
- '''
- self._log.debug('Calling to_phasemap')
- assert self.dim[0] == 1 # only one layer!
- assert self.iform in (1, 2) # only float or int! Phase has to be 2D!
- return PhaseMap(self.a, self.data[0, ...])
-
- @classmethod
- def from_magdata(self, mag_data, proj_axis='z', ax_slice=0, title='PYRAMID-MagData'):
- '''Export info from a :class:`~.MagData` slice to a :class:`~.SemperFormat` object.
-
- Parameters
- ----------
- mag_data : :class:`~.PhaseMap`
- Magnetic distribution object from which a slice should be converted.
- proj_axis : {'z', 'y', 'x'}, optional
- The axis, from which the slice is taken. The default is 'z'.
- ax_slice : int, optional
- The slice-index of the axis specified in `proj_axis`. Defaults to zero (first slice).
- title : string, optional
- Title of the file (not to be confused with the filename).
-
- Returns
- -------
- semper : :class:`~.SemperFormat` (N=1)
- Semper file format object containing the loaded information.
-
- '''
- self._log.debug('Calling from_magdata')
- # Find slice:
- assert proj_axis == 'z' or proj_axis == 'y' or proj_axis == 'x', \
- 'Axis has to be x, y or z (as string).'
- if proj_axis == 'z': # Slice of the xy-plane with z = ax_slice
- self._log.debug('proj_axis == z')
- u_mag = np.copy(mag_data.magnitude[0][ax_slice, ...]) # x-component
- v_mag = np.copy(mag_data.magnitude[1][ax_slice, ...]) # y-component
- elif proj_axis == 'y': # Slice of the xz-plane with y = ax_slice
- self._log.debug('proj_axis == y')
- u_mag = np.copy(mag_data.magnitude[0][:, ax_slice, :]) # x-component
- v_mag = np.copy(mag_data.magnitude[2][:, ax_slice, :]) # z-component
- elif proj_axis == 'x': # Slice of the yz-plane with x = ax_slice
- self._log.debug('proj_axis == x')
- u_mag = np.swapaxes(np.copy(mag_data.magnitude[2][..., ax_slice]), 0, 1) # z-component
- v_mag = np.swapaxes(np.copy(mag_data.magnitude[1][..., ax_slice]), 0, 1) # y-component
- # Create data field:
- data = np.expand_dims(u_mag, axis=0) + 1j*np.expand_dims(v_mag, axis=0)
-# np.flipud(data) # for semper the origin must be in the first line! # TODO: ???
- arg_dict = {}
- arg_dict['dim'] = data.shape
- arg_dict['a'] = mag_data.a
- arg_dict['data'] = data
- arg_dict['ICLASS'] = 1 # image
- arg_dict['IFORM'] = 3 # complex
- arg_dict['IVERSN'] = 2 # current standard
- arg_dict['ILABEL'] = 1 # True
- arg_dict['IFORMAT'] = None # not needed
- arg_dict['title'] = title
- arg_dict['IWP'] = 0 # seems standard
- arg_dict['IPLTYP'] = 248 # seems standard
- arg_dict['date'] = strftime('%y-%m-%d %H:%M:%S')
- arg_dict['ICCOLN'] = data.shape[2]//2 + 1
- arg_dict['ICROWN'] = data.shape[1]//2 + 1
- arg_dict['ICLAYN'] = 1
- return SemperFormat(arg_dict)
-
- def to_magdata(self):
- '''Export info from a :class:`~.SemperFormat` object to a :class:`~.MagData` slice.
-
- Parameters
- ----------
- None
-
- Returns
- -------
- mag_data : :class:`~.PhaseMap`
- The created magnetic distribution object.
-
- Notes
- -----
- Only works if the `iform` parameter is `3` (complex values).
-
- '''
- self._log.debug('Calling to_magdata')
- assert self.dim[0] == 1 # only one layer!
- assert self.iform == 3 # Magnetic slice is described by complex number!
- return MagData(self.a, np.array((self.data.real, self.data.imag, np.zeros(self.dim))))
-
- def convert_to_abs(self):
- '''Take the absolute of the data. Converts complex to float in the process.
-
- Parameters
- ----------
- None
-
- Returns
- -------
- None
-
- Notes
- -----
- Operates in place!
-
- '''
- self.data = np.abs(self.data) # usable for float and complex values!
- self.iform = 2 # update the format (now it's definitely float)!
-
- def print_info(self):
- '''Print all flag information of the :class:`.~SemperFormat` object.
-
- Parameters
- ----------
- None
-
- Returns
- -------
- None
-
- '''
- self._log.debug('Calling print_info')
- print '\n------------------------------------------------------'
- print self.title
- print self.date, '\n'
- print 'dimensions:', self.dim
- print 'grid spacing:', self.a
- print 'data range:', (self.data.min(), self.data.max()), '\n'
- print 'ICLASS: ', self.ICLASS_DICT[self.iclass]
- print 'IFORM : ', self.IFORM_DICT[self.iform]
- print 'IVERSN: ', self.iversn
- print 'ILABEL: ', self.ilabel == 1
- if self.iformat is not None:
- print 'IFORMAT:', self.iformat
- if self.ilabel:
- print 'IWP : ', self.iwp
- print 'ICCOLN: ', self.iccoln
- print 'ICROWN: ', self.icrown
- print 'ICLAYN: ', self.iclayn
- print '------------------------------------------------------\n'
diff --git a/pyramid/tests/pep8_log.txt b/pyramid/tests/pep8_log.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfb9880b6acab9de6225019ed0c41ed109800676
--- /dev/null
+++ b/pyramid/tests/pep8_log.txt
@@ -0,0 +1,143 @@
+<<< PEP8 LOGFILE >>>
+RUN: 2015-09-23 16:27:33
+IGNORED RULES: E125, E226, E228
+MAX LINE LENGTH: 99
+
+ERRORS AND WARNINGS:
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_dat.py:14:45: E261 at least two spaces before inline comment
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_dat.py:14:45: E262 inline comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_dat.py:18:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_dat.py:19:1: E302 expected 2 blank lines, found 1
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_dat.py:68:1: W391 blank line at end of file
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:81:1: E302 expected 2 blank lines, found 1
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:103:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:104:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:105:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:107:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:108:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:109:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:111:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:112:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:120:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:132:5: E303 too many blank lines (2)
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:140:1: E112 expected an indented block
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:141:1: E112 expected an indented block
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:142:1: E112 expected an indented block
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:143:1: E112 expected an indented block
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:144:1: E112 expected an indented block
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\magdata\magdata_from_vtk.py:155:35: W292 no newline at end of file
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_from_dm3.py:30:1: E112 expected an indented block
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_from_dm3.py:32:41: E261 at least two spaces before inline comment
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_from_dm3.py:32:41: E262 inline comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_tilt_series.py:29:31: E261 at least two spaces before inline comment
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_tilt_series.py:29:31: E262 inline comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_tilt_series.py:31:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_tilt_series.py:32:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_tilt_series.py:34:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_tilt_series.py:35:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_tilt_series.py:36:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\phasemap\phasemap_tilt_series.py:59:30: W292 no newline at end of file
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:37:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:38:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:39:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:40:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:41:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:42:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:43:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:44:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:45:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:46:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:47:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:48:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:49:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:50:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:51:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:52:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:53:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:54:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:55:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:56:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:57:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:58:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:59:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:60:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:61:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:62:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:63:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:64:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:65:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:66:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:67:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:68:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:69:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:70:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:71:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:72:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:73:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:74:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:75:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:76:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:77:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\bielefeld.py:87:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\custom_colormap.py:120:14: E128 continuation line under-indented for visual indent
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\custom_colormap.py:126:14: E128 continuation line under-indented for visual indent
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\impact_2D_test.py:40:100: E501 line too long (103 > 99 characters)
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:15:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:24:1: E302 expected 2 blank lines, found 1
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:49:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:83:3: E225 missing whitespace around operator
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:86:44: E225 missing whitespace around operator
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:91:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:93:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:94:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:95:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:96:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:97:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:101:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:102:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:108:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:108:1: E303 too many blank lines (3)
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:109:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:110:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:111:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:114:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:115:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:117:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:118:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:119:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:121:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:122:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:123:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:126:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:127:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\quiver_plot_enhanced.py:127:36: W292 no newline at end of file
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\test_multiprocessing_main.py:42:68: E261 at least two spaces before inline comment
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\test_multiprocessing_main.py:42:68: E262 inline comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\test_multiprocessing_main.py:42:100: E501 line too long (104 > 99 characters)
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\test_multiprocessing_main.py:51:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\test_multiprocessing_main.py:53:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\test_multiprocessing_main.py:58:68: E261 at least two spaces before inline comment
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\test_multiprocessing_main.py:58:68: E262 inline comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\test_multiprocessing_main.py:66:68: E261 at least two spaces before inline comment
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\test_multiprocessing_main.py:66:68: E262 inline comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\warning_control.py:16:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\visualization\paper 2\paper2_part2_simulation.py:120:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\visualization\paper 2\paper2_part3_experiment.py:100:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\visualization\pico 2015\poster_pico2015_2d.py:162:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\visualization\pico 2015\poster_pico2015_3d.py:56:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\visualization\pico 2015\poster_pico2015_3d.py:57:1: E265 block comment should start with '# '
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\visualization\pico 2015\poster_pico2015_3d.py:69:1: E265 block comment should start with '# '
+----> 123 PEP8 violations detected!
+
+TODOS:
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\pyramid\dataset.py: Supress annoying warning from traits!
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\pyramid\magdata.py: Supress annoying warning from traits!
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\pyramid\phasemapper.py: Why minus?
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\pyramid\phasemapper.py: Implement right!
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\pyramid\phasemapper.py: check if projector manages scalar multiplication (problem with MagData) and fix!
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\pyramid\semper.py: ???
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\pyramid\tests\test_projector.py: Test RotTiltProjector!!!
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\reconstruction\reconstruction_3d_from_magdata.py: toggle multiprocessing if nprocs > 1
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\scripts\temp\custom_colormap.py: Docstring!
+C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\pyramid\tests\test_projector.py: Test RotTiltProjector!!!
+----> 10 TODOs found!
diff --git a/scripts/gui/phasemap_creator.py b/scripts/gui/phasemap_creator.py
new file mode 100644
index 0000000000000000000000000000000000000000..8713c767a990d8f31034c52d0b9a6cab9e1f666a
--- /dev/null
+++ b/scripts/gui/phasemap_creator.py
@@ -0,0 +1,287 @@
+# -*- coding: utf-8 -*-
+
+# Form implementation generated from reading ui file 'phasemap_creator.ui'
+#
+# Created: Thu Sep 24 11:42:11 2015
+# by: PyQt4 UI code generator 4.9.6
+#
+# WARNING! All changes made in this file will be lost!
+
+
+import os
+import sys
+
+import numpy as np
+
+from PyQt4 import QtCore, QtGui
+
+from matplotlibwidget import MatplotlibWidget
+
+from PIL import Image
+from pyramid import PhaseMap
+import ercpy
+
+
+try:
+ _fromUtf8 = QtCore.QString.fromUtf8
+except AttributeError:
+ def _fromUtf8(s):
+ return s
+
+try:
+ _encoding = QtGui.QApplication.UnicodeUTF8
+
+ def _translate(context, text, disambig):
+ return QtGui.QApplication.translate(context, text, disambig, _encoding)
+except AttributeError:
+
+ def _translate(context, text, disambig):
+ return QtGui.QApplication.translate(context, text, disambig)
+
+
+class UI_PhaseMapCreatorMain(QtGui.QWidget):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ Form = self
+ self.setGeometry(100, 100, 900, 900)
+ self.setWindowTitle('PhaseMap Creator')
+ Form.setObjectName(_fromUtf8('PhaseMap Creator'))
+ ###########################################################################################
+ self.verticalLayout = QtGui.QVBoxLayout(Form)
+ self.verticalLayout.setObjectName(_fromUtf8("verticalLayout"))
+ self.mplwidget = MatplotlibWidget(Form)
+ self.mplwidget.setObjectName(_fromUtf8("mplwidget"))
+ self.verticalLayout.addWidget(self.mplwidget)
+ self.horizontalLayout = QtGui.QHBoxLayout()
+ self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
+ self.pushButton_phase = QtGui.QPushButton(Form)
+ self.pushButton_phase.setObjectName(_fromUtf8("pushButton_phase"))
+ self.horizontalLayout.addWidget(self.pushButton_phase)
+ self.pushButton_mask = QtGui.QPushButton(Form)
+ self.pushButton_mask.setObjectName(_fromUtf8("pushButton_mask"))
+ self.horizontalLayout.addWidget(self.pushButton_mask)
+ self.pushButton_conf = QtGui.QPushButton(Form)
+ self.pushButton_conf.setObjectName(_fromUtf8("pushButton_conf"))
+ self.horizontalLayout.addWidget(self.pushButton_conf)
+ self.pushButton_export = QtGui.QPushButton(Form)
+ self.pushButton_export.setObjectName(_fromUtf8("pushButton_export"))
+ self.horizontalLayout.addWidget(self.pushButton_export)
+ self.verticalLayout.addLayout(self.horizontalLayout)
+ self.horizontalLayout_2 = QtGui.QHBoxLayout()
+ self.horizontalLayout_2.setObjectName(_fromUtf8("horizontalLayout_2"))
+ self.label_a = QtGui.QLabel(Form)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Preferred)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.label_a.sizePolicy().hasHeightForWidth())
+ self.label_a.setSizePolicy(sizePolicy)
+ self.label_a.setObjectName(_fromUtf8("label_a"))
+ self.horizontalLayout_2.addWidget(self.label_a)
+ self.doubleSpinBox_a = QtGui.QDoubleSpinBox(Form)
+ self.doubleSpinBox_a.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignTrailing |
+ QtCore.Qt.AlignVCenter)
+ self.doubleSpinBox_a.setMaximum(1000)
+ self.doubleSpinBox_a.setProperty("value", 1)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.doubleSpinBox_a.sizePolicy().hasHeightForWidth())
+ self.doubleSpinBox_a.setSizePolicy(sizePolicy)
+ self.doubleSpinBox_a.setObjectName(_fromUtf8("doubleSpinBox_a"))
+ self.horizontalLayout_2.addWidget(self.doubleSpinBox_a)
+ self.label_thres = QtGui.QLabel(Form)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Preferred)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.label_thres.sizePolicy().hasHeightForWidth())
+ self.label_thres.setSizePolicy(sizePolicy)
+ self.label_thres.setObjectName(_fromUtf8("label_thres"))
+ self.horizontalLayout_2.addWidget(self.label_thres)
+ self.doubleSpinBox_thres = QtGui.QDoubleSpinBox(Form)
+ self.doubleSpinBox_thres.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignTrailing |
+ QtCore.Qt.AlignVCenter)
+ self.doubleSpinBox_thres.setMaximum(0)
+ self.doubleSpinBox_thres.setProperty("value", 0)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Minimum, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.doubleSpinBox_thres.sizePolicy().hasHeightForWidth())
+ self.doubleSpinBox_thres.setSizePolicy(sizePolicy)
+ self.doubleSpinBox_thres.setObjectName(_fromUtf8("doubleSpinBox_thres"))
+ self.horizontalLayout_2.addWidget(self.doubleSpinBox_thres)
+ self.horizontalScrollBar = QtGui.QScrollBar(Form)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.MinimumExpanding, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.horizontalScrollBar.sizePolicy().hasHeightForWidth())
+ self.horizontalScrollBar.setSizePolicy(sizePolicy)
+ self.horizontalScrollBar.setOrientation(QtCore.Qt.Horizontal)
+ self.horizontalScrollBar.setMaximum(0)
+ self.horizontalScrollBar.setObjectName(_fromUtf8("horizontalScrollBar"))
+ self.horizontalLayout_2.addWidget(self.horizontalScrollBar)
+ self.checkBox_mask = QtGui.QCheckBox(Form)
+ self.checkBox_mask.setChecked(True)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.checkBox_mask.sizePolicy().hasHeightForWidth())
+ self.checkBox_mask.setSizePolicy(sizePolicy)
+ self.checkBox_mask.setObjectName(_fromUtf8("checkBox_mask"))
+ self.horizontalLayout_2.addWidget(self.checkBox_mask)
+ self.checkBox_conf = QtGui.QCheckBox(Form)
+ self.checkBox_conf.setChecked(True)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.checkBox_conf.sizePolicy().hasHeightForWidth())
+ self.checkBox_conf.setSizePolicy(sizePolicy)
+ self.checkBox_conf.setObjectName(_fromUtf8("checkBox_conf"))
+ self.horizontalLayout_2.addWidget(self.checkBox_conf)
+ self.verticalLayout.addLayout(self.horizontalLayout_2)
+ ###########################################################################################
+ self.retranslateUi(Form)
+ # CONNECTS:
+ self.connect(self.pushButton_phase, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.load_phase)
+ self.connect(self.pushButton_mask, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.load_mask)
+ self.connect(self.pushButton_conf, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.load_conf)
+ self.connect(self.pushButton_export, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.export)
+ self.connect(self.horizontalScrollBar, QtCore.SIGNAL(_fromUtf8("valueChanged(int)")),
+ self.doubleSpinBox_thres.setValue)
+ self.connect(self.doubleSpinBox_thres, QtCore.SIGNAL(_fromUtf8("valueChanged(double)")),
+ self.horizontalScrollBar.setValue)
+ self.connect(self.checkBox_mask, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.update_phasemap)
+ self.connect(self.checkBox_conf, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.update_phasemap)
+ self.connect(self.doubleSpinBox_a, QtCore.SIGNAL(_fromUtf8('editingFinished()')),
+ self.update_phasemap)
+ self.connect(self.doubleSpinBox_thres, QtCore.SIGNAL(_fromUtf8('valueChanged(double)')),
+ self.update_mask)
+ QtCore.QMetaObject.connectSlotsByName(Form)
+ # OTHER STUFF:
+ self.mplwidget.axes.set_visible(False)
+ self.mplwidget.axes.set_visible(False)
+ self.mplwidget.axes.set_visible(False)
+ self.pushButton_mask.setEnabled(False)
+ self.pushButton_conf.setEnabled(False)
+ self.pushButton_export.setEnabled(False)
+ self.doubleSpinBox_thres.setEnabled(False)
+ self.horizontalScrollBar.setEnabled(False)
+ self.phase_loaded = False
+ self.mask_loaded = False
+ self.dir = ''
+
+ def retranslateUi(self, Form):
+ ###########################################################################################
+ Form.setWindowTitle(_translate("Form", "PhaseMap Creator", None))
+ self.pushButton_phase.setText(_translate("Form", "Load Phase", None))
+ self.pushButton_mask.setText(_translate("Form", "Load Mask", None))
+ self.pushButton_conf.setText(_translate("Form", "Load Confidence", None))
+ self.pushButton_export.setText(_translate("Form", "Export PhaseMap", None))
+ self.label_a.setText(_translate("Form", "Grid Spacing [nm]:", None))
+ self.label_thres.setText(_translate("Form", "Mask Threshold:", None))
+ self.checkBox_mask.setText(_translate("Form", "show mask", None))
+ self.checkBox_conf.setText(_translate("Form", "show confidence", None))
+ ###########################################################################################
+
+ def update_phasemap(self):
+ if self.phase_loaded:
+ self.phase_map.a = self.doubleSpinBox_a.value()
+ show_mask = self.checkBox_mask.isChecked()
+ show_conf = self.checkBox_conf.isChecked()
+ self.mplwidget.axes.clear()
+ self.mplwidget.axes.hold(True)
+ self.phase_map.display_phase('PhaseMap', axis=self.mplwidget.axes,
+ show_mask=show_mask, show_conf=show_conf, cbar=False)
+ self.mplwidget.draw()
+
+ def update_mask(self):
+ if self.mask_loaded:
+ threshold = self.doubleSpinBox_thres.value()
+ mask = np.asarray(Image.fromarray(self.emd['mask']).resize(self.emd['phase'].shape))
+ self.phase_map.mask = np.where(mask >= threshold, True, False)
+ self.update_phasemap()
+
+ def load_phase(self):
+ try:
+ self.phase_path = QtGui.QFileDialog.getOpenFileName(self, 'Load Phase', self.dir)
+ self.emd = ercpy.EMD()
+ self.emd.add_signal_from_file(self.phase_path, name='phase')
+ except ValueError:
+ return # Abort if no phase_path is selected!
+ if self.emd.signals['phase'].axes_manager[0].scale != 1.:
+ self.doubleSpinBox_a.setValue(self.emd.signals['phase'].axes_manager[0].scale)
+ self.dir = os.path.join(os.path.dirname(self.phase_path))
+ self.phase_map = PhaseMap(self.doubleSpinBox_a.value(), self.emd['phase'])
+ self.mplwidget.axes.set_visible(True)
+ self.mplwidget.axes.set_visible(True)
+ self.mplwidget.axes.set_visible(True)
+ self.pushButton_mask.setEnabled(True)
+ self.pushButton_conf.setEnabled(True)
+ self.pushButton_export.setEnabled(True)
+ self.phase_loaded = True
+ self.horizontalScrollBar.setMinimum(0)
+ self.horizontalScrollBar.setMaximum(0)
+ self.horizontalScrollBar.setEnabled(False)
+ self.doubleSpinBox_thres.setMinimum(0)
+ self.doubleSpinBox_thres.setMaximum(0)
+ self.doubleSpinBox_thres.setValue(0)
+ self.doubleSpinBox_thres.setEnabled(False)
+ self.mask_loaded = False
+ self.update_phasemap()
+
+ def load_mask(self):
+ try:
+ mask_path = QtGui.QFileDialog.getOpenFileName(self, 'Load Mask', self.dir)
+ self.emd.add_signal_from_file(mask_path, name='mask')
+ except ValueError:
+ return # Abort if no mask_path is selected!
+ mask_min = self.emd['mask'].min()
+ mask_max = self.emd['mask'].max()
+ self.horizontalScrollBar.setEnabled(True)
+ self.horizontalScrollBar.setMinimum(mask_min)
+ self.horizontalScrollBar.setMaximum(mask_max)
+ self.horizontalScrollBar.setSingleStep((mask_max-mask_min)/255.)
+ self.horizontalScrollBar.setValue((mask_max-mask_min)/2.)
+ self.doubleSpinBox_thres.setEnabled(True)
+ self.doubleSpinBox_thres.setMinimum(mask_min)
+ self.doubleSpinBox_thres.setMaximum(mask_max)
+ self.doubleSpinBox_thres.setSingleStep((mask_max-mask_min)/255.)
+ self.doubleSpinBox_thres.setValue((mask_max-mask_min)/2.)
+ self.mask_loaded = True
+ self.update_mask()
+
+ def load_conf(self):
+ try:
+ conf_path = QtGui.QFileDialog.getOpenFileName(self, 'Load Confidence', self.dir)
+ except ValueError:
+ return # Abort if no conf_path is selected!
+ self.emd.add_signal_from_file(conf_path, name='confidence')
+ confidence = self.emd['confidence'] / self.emd['confidence'].max()
+ confidence = np.asarray(Image.fromarray(confidence).resize(self.emd['phase'].shape))
+ self.phase_map.confidence = confidence
+ self.update_phasemap()
+
+ def export(self):
+ try:
+ export_name = os.path.splitext(os.path.basename(self.phase_path))[0]
+ export_default = os.path.join(self.dir, 'phasemap_gui_{}.nc'.format(export_name))
+ export_path = QtGui.QFileDialog.getSaveFileName(self, 'Export PhaseMap',
+ export_default,
+ 'EMD/NetCDF4 (*.emd *.nc)')
+ if export_path.endswith('.nc'):
+ self.phase_map.save_to_netcdf4(export_path)
+ elif export_path.endswith('.emd'):
+ self.emd.save_to_emd(export_path)
+ except ValueError:
+ return # Abort if no export_path is selected!
+
+if __name__ == '__main__':
+ app = QtGui.QApplication(sys.argv)
+ widget = UI_PhaseMapCreatorMain()
+ widget.show()
+ sys.exit(app.exec_())
diff --git a/scripts/gui/phasemap_creator.ui b/scripts/gui/phasemap_creator.ui
new file mode 100644
index 0000000000000000000000000000000000000000..80c739104dd0b1949b8d01363c8c453b363e2147
--- /dev/null
+++ b/scripts/gui/phasemap_creator.ui
@@ -0,0 +1,209 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>Form</class>
+ <widget class="QWidget" name="Form">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>789</width>
+ <height>775</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>Form</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="MatplotlibWidget" name="mplwidget"/>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <widget class="QPushButton" name="pushButton_phase">
+ <property name="text">
+ <string>Load Phase</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_mask">
+ <property name="text">
+ <string>Load Mask</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_conf">
+ <property name="text">
+ <string>Load Confidence</string>
+ </property>
+ <property name="checkable">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="pushButton_export">
+ <property name="text">
+ <string>Export Phasemap</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item>
+ <layout class="QHBoxLayout" name="horizontalLayout_2">
+ <item>
+ <widget class="QLabel" name="label_2">
+ <property name="text">
+ <string>Grid spacing [nm]:</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QDoubleSpinBox" name="doubleSpinBox_2">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>60</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="baseSize">
+ <size>
+ <width>0</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+ </property>
+ <property name="maximum">
+ <double>1000.000000000000000</double>
+ </property>
+ <property name="value">
+ <double>1.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>Mask Threshold:</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QDoubleSpinBox" name="doubleSpinBox">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>60</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="maximumSize">
+ <size>
+ <width>16777215</width>
+ <height>16777215</height>
+ </size>
+ </property>
+ <property name="baseSize">
+ <size>
+ <width>0</width>
+ <height>0</height>
+ </size>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+ </property>
+ <property name="prefix">
+ <string/>
+ </property>
+ <property name="decimals">
+ <number>2</number>
+ </property>
+ <property name="maximum">
+ <double>0.000000000000000</double>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QScrollBar" name="horizontalScrollBar">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="MinimumExpanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximum">
+ <number>0</number>
+ </property>
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBox_mask">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>show mask</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="checkBox_conf">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="text">
+ <string>show confidence</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ <customwidgets>
+ <customwidget>
+ <class>MatplotlibWidget</class>
+ <extends>QWidget</extends>
+ <header>matplotlibwidget</header>
+ </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>