Module wsp_tools.sitie
Contains utilities for reconstructing phase and magnetization from Lorentz images.
The most common use case is to generate a lorentz object from a .dm3 file.
Then you can analyze using high_pass(), sitie(), clip_data(), etc.
Example:
import ncempy.io.dm as dm
import wsp_tools as wt
fname = '/path/to/data.dm3'
dm3file = dm.dmReader(fname)
img = wt.lorentz(dm3file)
img.sitie(defocus=1e-3)
img.phase.clip_data(sigma=5).high_pass().low_pass()
img.Bx.clip_data(sigma=5).high_pass().low_pass()
img.By.clip_data(sigma=5).high_pass().low_pass()
img.saveMeta(outdir='someDirectory') # Saves defocus, pixelSize, etc
### plot img.Bx, img.By, img.phase, img.data, img.rawData, etc
Expand source code
# wsp-tools is TEM data analysis and simulation tools developed by WSP as a grad student in the McMorran Lab.
# Copyright (C) 2021 William S. Parker
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""Contains utilities for reconstructing phase and magnetization from Lorentz images.
The most common use case is to generate a lorentz object from a ```.dm3``` file.
Then you can analyze using high_pass(), sitie(), clip_data(), etc.
Example:
```python
import ncempy.io.dm as dm
import wsp_tools as wt
fname = '/path/to/data.dm3'
dm3file = dm.dmReader(fname)
img = wt.lorentz(dm3file)
img.sitie(defocus=1e-3)
img.phase.clip_data(sigma=5).high_pass().low_pass()
img.Bx.clip_data(sigma=5).high_pass().low_pass()
img.By.clip_data(sigma=5).high_pass().low_pass()
img.saveMeta(outdir='someDirectory') # Saves defocus, pixelSize, etc
### plot img.Bx, img.By, img.phase, img.data, img.rawData, etc
```
"""
# %%
import numpy as np
import matplotlib.pyplot as plt
import os
from deprecated import deprecated
from . import image_processing as ip
from .pyplotwrapper import subplots
from . import constants as _
from .ltem import phase_from_img, ind_from_phase
np.seterr(divide='ignore', invalid='ignore')
import json
__all__ = ['Lorentz','lorentz','B_from_phase','SITIE']
@deprecated(version='1.2.0', reason='This function has not found much use and will not be maintained')
def save_lorentz(img, fname=None, fdir=''):
"""DEPRECATED. This function will no longer be maintained.
Saves a `lorentz` object as a `.npz` archive.
**Parameters**
* **img** : _lorentz_ <br />
The lorentz object to save.
* **fname** : _string, optional_ <br />
If not given, the output will be the filename in the lorentz object metadata, with `.npz` rather than `.dm3`.
* **fdir** : _string, optional_ <br />
The directory where the lorentz object will be saved. <br />
Default is `fdir = ''`.
**Returns**
* **None**
"""
if fname is None:
fname = os.path.splitext(img.metadata['filename'])[0]
if not os.path.exists(fdir):
if not fdir == '':
os.makedirs(fdir)
np.savez(os.path.join(fdir, fname), **img.__dict__)
return(None)
@deprecated(version='1.2.0', reason='This function has not found much use and will not be maintained')
def load_lorentz(fname):
"""DEPRECATED. This function will no longer be maintained.
Loads a `lorentz` object that has been saved as a `.npz` via `save_lorentz()`.
**Parameters**
* **fname** : _string_ <br />
**Returns**
* **img** : _lorentz_ <br />
The saved lorentz object, converted from a `.npz`.
"""
f = np.load(fname, allow_pickle=True)
fm = f['metadata'].item()
dm3 = {'data':f['data'], 'pixelSize':[fm['pixelSize'],fm['pixelSize']], 'pixelUnit':[fm['pixelUnit'],fm['pixelUnit']], 'filename':fm['filename']}
img = lorentz(dm3)
img.phase = ip.ndap(f['phase'])
img.Bx = ip.ndap(f['Bx'])
img.By = ip.ndap(f['By'])
img.x = f['x']
img.y = f['y']
fm.update(img.metadata)
img.metadata.update(fm)
return(img)
def lorentz(file):
"""Creates a `Lorentz` class instance for each image in a `.dm3` sequence.
This function essentially acts as a wrapper for the `Lorentz` class, adding an extra handler
for `.dm3` image sequences. When the `.dm3` file contains a sequence of images, it is split into
individual `Lorentz` instances.
**Parameters**
* **dm3file** : _dictionary-like_ <br />
a dm3-like file with the following keys: <br />
<ul>
<li> **data** : _ndarray_ <br />
An array carrying the electron counts. </li>
<li> **pixelSize** : _tuple_ <br />
(_number_, _number_) - the x and y pixel sizes. </li>
<li> **pixelUnit** : _tuple_ <br />
(_string_, _string_) - the x and y pixel units. </li>
<li> **filename** : _string_ <br /></li>
</ul>
**Returns**
* **out** : _list, Lorentz_ <br />
a list of `wsp-tools.sitie.Lorentz` instances, if the `.dm3` file is an image sequence.
Otherwise, a single `wsp-tools.sitie.Lorentz` instance.
"""
if len(file['data'].shape) <= 2:
return Lorentz(file)
else:
f1 = file.copy()
out = []
for dataset in file['data']:
f1['data'] = dataset
f1['pixelSize'] = [file['pixelSize'][-2], file['pixelSize'][-1]]
f1['pixelUnit'] = [file['pixelUnit'][-2], file['pixelUnit'][-1]]
f1['coords'] = [file['coords'][-2], file['coords'][-1]]
out.append(Lorentz(f1))
return(out)
class Lorentz:
"""Class that contains sitie information about a lorentz image.
**Parameters**
* **dm3file** : _dictionary-like_ <br />
a dm3-like file with the following keys: <br />
<ul>
<li> **data** : _ndarray_ <br />
An array carrying the electron counts. </li>
<li> **pixelSize** : _tuple_ <br />
(_number_, _number_) - the x and y pixel sizes. </li>
<li> **pixelUnit** : _tuple_ <br />
(_string_, _string_) - the x and y pixel units. </li>
<li> **filename** : _string_ <br /></li>
</ul>
"""
def __init__(self, dm3file):
self.data = ip.ndap(dm3file['data'])
self.dx = dm3file['pixelSize'][0]
self.dy = dm3file['pixelSize'][1]
self.xUnit = dm3file['pixelUnit'][0]
self.yUnit = dm3file['pixelUnit'][1]
self.x = np.arange(0,self.data.shape[1]) * self.dx
self.y = np.arange(0,self.data.shape[0]) * self.dy
self.metadata = {
'dx':float(dm3file['pixelSize'][0]),
'dy':float(dm3file['pixelSize'][1]),
'xUnit':dm3file['pixelUnit'][0],
'yUnit':dm3file['pixelUnit'][1],
'filename':dm3file['filename']
}
self.phase = None
self.Bx, self.By = None, None
self.fix_units()
def fix_units(self, xunit=None, yunit=None):
"""Change the pixel units to meters.
**Parameters**
* **unit** : _number, optional_ <br />
The scale to multiply values by (i.e., going from 'µm' to 'm', you would use `unit = 1e-6`). If none is given, `fix_units` will try to convert from `self.pixelUnit` to meters.
**Returns**
* **self** : _lorentz_
"""
if xunit is None:
if self.xUnit == 'nm':
xunit = 1e-9
elif self.xUnit == 'mm':
xunit = 1e-3
elif self.xUnit == 'µm':
xunit = 1e-6
elif self.xUnit == 'm':
xunit = 1
else:
xunit = 1
if yunit is None:
if self.yUnit == 'nm':
yunit = 1e-9
elif self.yUnit == 'mm':
yunit = 1e-3
elif self.yUnit == 'µm':
yunit = 1e-6
elif self.yUnit == 'm':
yunit = 1
else:
yunit = 1
self.dx *= xunit
self.dy *= yunit
self.xUnit = 'm'
self.yUnit = 'm'
self.x *= xunit
self.y *= yunit
self.metadata.update({
'dx': float(self.dx),
'dy': float(self.dy),
'xUnit': self.xUnit,
'yUnit': self.yUnit
})
return(None)
def sitie(self, defocus = 1, thickness = 60e-9, wavelength=1.97e-12):
"""Carries out phase and B-field reconstruction.
Assigns phase, Bx, and By attributes.
Updates metadata with the defocus and wavelength.
**Parameters**
* **defocus** : _number, optional_ <br />
The defocus at which the images were taken. <br />
Default is `defocus = 1`.
* **wavelength** : _number, optional_ <br />
The electron wavelength. <br />
Default is `wavelength = 1.96e-12` (relativistic wavelength of a 300kV electron).
**Returns**
* **self** : _lorentz_
"""
self.metadata.update({'defocus': defocus, 'wavelength': wavelength, 'thickness': thickness})
self.phase = ip.ndap(phase_from_img(self.data, defocus, self.dx, self.dy, wavelength))
self.Bx, self.By = [ip.ndap(arr) for arr in ind_from_phase(self.phase, thickness)]
return(None)
def preview(self, window=None):
"""Preview the image.
Note that unlike `pyplotwrapper`, window is in units of pixels.
**Parameters**
* **window** : _array-like, optional_ <br />
Format is `window = (xmin, xmax, ymin, ymax)`. <br />
Default is `window = (0, -1, 0, -1)`
"""
fig, ax = subplots(11)
if not window is None:
ax[0,0].setWindow(window)
data = ip.clip_data(self.data, sigma=10)
ax[0,0].setAxes(self.x, self.y)
ax[0,0].set_xlabel("x ({:})".format(self.dx))
ax[0,0].set_ylabel("y ({:})".format(self.dy))
ax[0,0].imshow(data)
plt.show()
def saveMeta(self, outdir='', outname='metadata.json'):
"""Save the metadata of the lorentz object to a file.
**Parameters**
* **outdir** : _string, optional_ <br />
The directory where you'd like to save the metadata. <br />
Default is `outdir = ''`.
* **outname** : _string, optional_ <br />
The name of the metadata file. <br />
Default is `outname = 'metadata.json'`.
"""
if not os.path.exists(outdir):
os.makedirs(outdir)
with open(os.path.join(outdir, outname), 'w') as fp:
json.dump(self.metadata, fp, indent="")
################################## SITIE #######################################
@deprecated(version='1.2.0', reason='You should now use wsp_tools.ltem.ind_from_phase. As of this version, B_from_phase just calls ind_from_phase.')
def B_from_phase(phase, thickness=1):
"""DEPRECATED. You should instead use `wsp_tools.ltem.ind_from_phase`.
Reconstructs the B-field from the phase profile.
**Parameters**
* **phase** : _ndarray_ <br />
a 2d array representing the electron's phase.
* **thickness** : _number_ <br />
the thickness of the sample. <br />
Default is `thickness = 1`.
**Returns**
* **Bx** : _ndarray_ <br />
The x-component of the magnetic field.
* **By** : _ndarray_ <br />
The y-component of the magnetic field.
"""
return(ind_from_phase(phase, thickness))
@deprecated(version='1.2.0', reason='You should now use wsp_tools.ltem.phase_from_img. As of this version, SITIE just calls phase_from_img.')
def SITIE(image, defocus, pixel_size = 1, wavelength=1.97e-12):
"""DEPRECATED. You should instead use `wsp_tools.ltem.phase_from_img`.
Reconstruct the phase from a defocussed image.
**Parameters**
* **image** : _ndarray_ <br />
the 2d image data. <br />
* **defocus** : _number_ <br />
* **pixel_size** : _number, optional_ <br />
Default is `pixel_size = 1`.
* **wavelength** : _number, optional_ <br />
Default is `wavelength = 1.97e-12` (the relativistic wavelength of a 300kV electron).
**Returns**
* **phase** : _ndarray_ <br />
"""
return(phase_from_img(img, defocus, pixel_size, pixel_size, wavelength))Functions
def B_from_phase(phase, thickness=1)-
DEPRECATED. You should instead use
ind_from_phase().Reconstructs the B-field from the phase profile.
Parameters
-
phase : ndarray
a 2d array representing the electron's phase. -
thickness : number
the thickness of the sample.
Default isthickness = 1.
Returns
-
Bx : ndarray
The x-component of the magnetic field. -
By : ndarray
The y-component of the magnetic field.
Expand source code
@deprecated(version='1.2.0', reason='You should now use wsp_tools.ltem.ind_from_phase. As of this version, B_from_phase just calls ind_from_phase.') def B_from_phase(phase, thickness=1): """DEPRECATED. You should instead use `wsp_tools.ltem.ind_from_phase`. Reconstructs the B-field from the phase profile. **Parameters** * **phase** : _ndarray_ <br /> a 2d array representing the electron's phase. * **thickness** : _number_ <br /> the thickness of the sample. <br /> Default is `thickness = 1`. **Returns** * **Bx** : _ndarray_ <br /> The x-component of the magnetic field. * **By** : _ndarray_ <br /> The y-component of the magnetic field. """ return(ind_from_phase(phase, thickness)) -
def SITIE(image, defocus, pixel_size=1, wavelength=1.97e-12)-
DEPRECATED. You should instead use
phase_from_img().Reconstruct the phase from a defocussed image.
Parameters
-
image : ndarray
the 2d image data. -
defocus : number
-
pixel_size : number, optional
Default ispixel_size = 1. -
wavelength : number, optional
Default iswavelength = 1.97e-12(the relativistic wavelength of a 300kV electron).
Returns
- phase : ndarray
Expand source code
@deprecated(version='1.2.0', reason='You should now use wsp_tools.ltem.phase_from_img. As of this version, SITIE just calls phase_from_img.') def SITIE(image, defocus, pixel_size = 1, wavelength=1.97e-12): """DEPRECATED. You should instead use `wsp_tools.ltem.phase_from_img`. Reconstruct the phase from a defocussed image. **Parameters** * **image** : _ndarray_ <br /> the 2d image data. <br /> * **defocus** : _number_ <br /> * **pixel_size** : _number, optional_ <br /> Default is `pixel_size = 1`. * **wavelength** : _number, optional_ <br /> Default is `wavelength = 1.97e-12` (the relativistic wavelength of a 300kV electron). **Returns** * **phase** : _ndarray_ <br /> """ return(phase_from_img(img, defocus, pixel_size, pixel_size, wavelength)) -
def lorentz(file)-
Creates a
Lorentzclass instance for each image in a.dm3sequence.This function essentially acts as a wrapper for the
Lorentzclass, adding an extra handler for.dm3image sequences. When the.dm3file contains a sequence of images, it is split into individualLorentzinstances.Parameters
- dm3file : dictionary-like
a dm3-like file with the following keys:
- data : ndarray
An array carrying the electron counts. - pixelSize : tuple
(number, number) - the x and y pixel sizes. - pixelUnit : tuple
(string, string) - the x and y pixel units. - filename : string
- data : ndarray
Returns * out : list, Lorentz
a list ofwsp-tools.sitie.Lorentzinstances, if the.dm3file is an image sequence. Otherwise, a singlewsp-tools.sitie.Lorentzinstance.Expand source code
def lorentz(file): """Creates a `Lorentz` class instance for each image in a `.dm3` sequence. This function essentially acts as a wrapper for the `Lorentz` class, adding an extra handler for `.dm3` image sequences. When the `.dm3` file contains a sequence of images, it is split into individual `Lorentz` instances. **Parameters** * **dm3file** : _dictionary-like_ <br /> a dm3-like file with the following keys: <br /> <ul> <li> **data** : _ndarray_ <br /> An array carrying the electron counts. </li> <li> **pixelSize** : _tuple_ <br /> (_number_, _number_) - the x and y pixel sizes. </li> <li> **pixelUnit** : _tuple_ <br /> (_string_, _string_) - the x and y pixel units. </li> <li> **filename** : _string_ <br /></li> </ul> **Returns** * **out** : _list, Lorentz_ <br /> a list of `wsp-tools.sitie.Lorentz` instances, if the `.dm3` file is an image sequence. Otherwise, a single `wsp-tools.sitie.Lorentz` instance. """ if len(file['data'].shape) <= 2: return Lorentz(file) else: f1 = file.copy() out = [] for dataset in file['data']: f1['data'] = dataset f1['pixelSize'] = [file['pixelSize'][-2], file['pixelSize'][-1]] f1['pixelUnit'] = [file['pixelUnit'][-2], file['pixelUnit'][-1]] f1['coords'] = [file['coords'][-2], file['coords'][-1]] out.append(Lorentz(f1)) return(out) - dm3file : dictionary-like
Classes
class Lorentz (dm3file)-
Class that contains sitie information about a lorentz image.
Parameters
- dm3file : dictionary-like
a dm3-like file with the following keys:
- data : ndarray
An array carrying the electron counts. - pixelSize : tuple
(number, number) - the x and y pixel sizes. - pixelUnit : tuple
(string, string) - the x and y pixel units. - filename : string
- data : ndarray
Expand source code
class Lorentz: """Class that contains sitie information about a lorentz image. **Parameters** * **dm3file** : _dictionary-like_ <br /> a dm3-like file with the following keys: <br /> <ul> <li> **data** : _ndarray_ <br /> An array carrying the electron counts. </li> <li> **pixelSize** : _tuple_ <br /> (_number_, _number_) - the x and y pixel sizes. </li> <li> **pixelUnit** : _tuple_ <br /> (_string_, _string_) - the x and y pixel units. </li> <li> **filename** : _string_ <br /></li> </ul> """ def __init__(self, dm3file): self.data = ip.ndap(dm3file['data']) self.dx = dm3file['pixelSize'][0] self.dy = dm3file['pixelSize'][1] self.xUnit = dm3file['pixelUnit'][0] self.yUnit = dm3file['pixelUnit'][1] self.x = np.arange(0,self.data.shape[1]) * self.dx self.y = np.arange(0,self.data.shape[0]) * self.dy self.metadata = { 'dx':float(dm3file['pixelSize'][0]), 'dy':float(dm3file['pixelSize'][1]), 'xUnit':dm3file['pixelUnit'][0], 'yUnit':dm3file['pixelUnit'][1], 'filename':dm3file['filename'] } self.phase = None self.Bx, self.By = None, None self.fix_units() def fix_units(self, xunit=None, yunit=None): """Change the pixel units to meters. **Parameters** * **unit** : _number, optional_ <br /> The scale to multiply values by (i.e., going from 'µm' to 'm', you would use `unit = 1e-6`). If none is given, `fix_units` will try to convert from `self.pixelUnit` to meters. **Returns** * **self** : _lorentz_ """ if xunit is None: if self.xUnit == 'nm': xunit = 1e-9 elif self.xUnit == 'mm': xunit = 1e-3 elif self.xUnit == 'µm': xunit = 1e-6 elif self.xUnit == 'm': xunit = 1 else: xunit = 1 if yunit is None: if self.yUnit == 'nm': yunit = 1e-9 elif self.yUnit == 'mm': yunit = 1e-3 elif self.yUnit == 'µm': yunit = 1e-6 elif self.yUnit == 'm': yunit = 1 else: yunit = 1 self.dx *= xunit self.dy *= yunit self.xUnit = 'm' self.yUnit = 'm' self.x *= xunit self.y *= yunit self.metadata.update({ 'dx': float(self.dx), 'dy': float(self.dy), 'xUnit': self.xUnit, 'yUnit': self.yUnit }) return(None) def sitie(self, defocus = 1, thickness = 60e-9, wavelength=1.97e-12): """Carries out phase and B-field reconstruction. Assigns phase, Bx, and By attributes. Updates metadata with the defocus and wavelength. **Parameters** * **defocus** : _number, optional_ <br /> The defocus at which the images were taken. <br /> Default is `defocus = 1`. * **wavelength** : _number, optional_ <br /> The electron wavelength. <br /> Default is `wavelength = 1.96e-12` (relativistic wavelength of a 300kV electron). **Returns** * **self** : _lorentz_ """ self.metadata.update({'defocus': defocus, 'wavelength': wavelength, 'thickness': thickness}) self.phase = ip.ndap(phase_from_img(self.data, defocus, self.dx, self.dy, wavelength)) self.Bx, self.By = [ip.ndap(arr) for arr in ind_from_phase(self.phase, thickness)] return(None) def preview(self, window=None): """Preview the image. Note that unlike `pyplotwrapper`, window is in units of pixels. **Parameters** * **window** : _array-like, optional_ <br /> Format is `window = (xmin, xmax, ymin, ymax)`. <br /> Default is `window = (0, -1, 0, -1)` """ fig, ax = subplots(11) if not window is None: ax[0,0].setWindow(window) data = ip.clip_data(self.data, sigma=10) ax[0,0].setAxes(self.x, self.y) ax[0,0].set_xlabel("x ({:})".format(self.dx)) ax[0,0].set_ylabel("y ({:})".format(self.dy)) ax[0,0].imshow(data) plt.show() def saveMeta(self, outdir='', outname='metadata.json'): """Save the metadata of the lorentz object to a file. **Parameters** * **outdir** : _string, optional_ <br /> The directory where you'd like to save the metadata. <br /> Default is `outdir = ''`. * **outname** : _string, optional_ <br /> The name of the metadata file. <br /> Default is `outname = 'metadata.json'`. """ if not os.path.exists(outdir): os.makedirs(outdir) with open(os.path.join(outdir, outname), 'w') as fp: json.dump(self.metadata, fp, indent="")Methods
def fix_units(self, xunit=None, yunit=None)-
Change the pixel units to meters.
Parameters
- unit : number, optional
The scale to multiply values by (i.e., going from 'µm' to 'm', you would useunit = 1e-6). If none is given,fix_unitswill try to convert fromself.pixelUnitto meters.
Returns
- self : lorentz
Expand source code
def fix_units(self, xunit=None, yunit=None): """Change the pixel units to meters. **Parameters** * **unit** : _number, optional_ <br /> The scale to multiply values by (i.e., going from 'µm' to 'm', you would use `unit = 1e-6`). If none is given, `fix_units` will try to convert from `self.pixelUnit` to meters. **Returns** * **self** : _lorentz_ """ if xunit is None: if self.xUnit == 'nm': xunit = 1e-9 elif self.xUnit == 'mm': xunit = 1e-3 elif self.xUnit == 'µm': xunit = 1e-6 elif self.xUnit == 'm': xunit = 1 else: xunit = 1 if yunit is None: if self.yUnit == 'nm': yunit = 1e-9 elif self.yUnit == 'mm': yunit = 1e-3 elif self.yUnit == 'µm': yunit = 1e-6 elif self.yUnit == 'm': yunit = 1 else: yunit = 1 self.dx *= xunit self.dy *= yunit self.xUnit = 'm' self.yUnit = 'm' self.x *= xunit self.y *= yunit self.metadata.update({ 'dx': float(self.dx), 'dy': float(self.dy), 'xUnit': self.xUnit, 'yUnit': self.yUnit }) return(None) - unit : number, optional
def preview(self, window=None)-
Preview the image.
Note that unlike
pyplotwrapper, window is in units of pixels.Parameters
- window : array-like, optional
Format iswindow = (xmin, xmax, ymin, ymax).
Default iswindow = (0, -1, 0, -1)
Expand source code
def preview(self, window=None): """Preview the image. Note that unlike `pyplotwrapper`, window is in units of pixels. **Parameters** * **window** : _array-like, optional_ <br /> Format is `window = (xmin, xmax, ymin, ymax)`. <br /> Default is `window = (0, -1, 0, -1)` """ fig, ax = subplots(11) if not window is None: ax[0,0].setWindow(window) data = ip.clip_data(self.data, sigma=10) ax[0,0].setAxes(self.x, self.y) ax[0,0].set_xlabel("x ({:})".format(self.dx)) ax[0,0].set_ylabel("y ({:})".format(self.dy)) ax[0,0].imshow(data) plt.show() - window : array-like, optional
def saveMeta(self, outdir='', outname='metadata.json')-
Save the metadata of the lorentz object to a file.
Parameters
-
outdir : string, optional
The directory where you'd like to save the metadata.
Default isoutdir = ''. -
outname : string, optional
The name of the metadata file.
Default isoutname = 'metadata.json'.
Expand source code
def saveMeta(self, outdir='', outname='metadata.json'): """Save the metadata of the lorentz object to a file. **Parameters** * **outdir** : _string, optional_ <br /> The directory where you'd like to save the metadata. <br /> Default is `outdir = ''`. * **outname** : _string, optional_ <br /> The name of the metadata file. <br /> Default is `outname = 'metadata.json'`. """ if not os.path.exists(outdir): os.makedirs(outdir) with open(os.path.join(outdir, outname), 'w') as fp: json.dump(self.metadata, fp, indent="") -
def sitie(self, defocus=1, thickness=6e-08, wavelength=1.97e-12)-
Carries out phase and B-field reconstruction.
Assigns phase, Bx, and By attributes.
Updates metadata with the defocus and wavelength.
Parameters
-
defocus : number, optional
The defocus at which the images were taken.
Default isdefocus = 1. -
wavelength : number, optional
The electron wavelength.
Default iswavelength = 1.96e-12(relativistic wavelength of a 300kV electron).
Returns
- self : lorentz
Expand source code
def sitie(self, defocus = 1, thickness = 60e-9, wavelength=1.97e-12): """Carries out phase and B-field reconstruction. Assigns phase, Bx, and By attributes. Updates metadata with the defocus and wavelength. **Parameters** * **defocus** : _number, optional_ <br /> The defocus at which the images were taken. <br /> Default is `defocus = 1`. * **wavelength** : _number, optional_ <br /> The electron wavelength. <br /> Default is `wavelength = 1.96e-12` (relativistic wavelength of a 300kV electron). **Returns** * **self** : _lorentz_ """ self.metadata.update({'defocus': defocus, 'wavelength': wavelength, 'thickness': thickness}) self.phase = ip.ndap(phase_from_img(self.data, defocus, self.dx, self.dy, wavelength)) self.Bx, self.By = [ip.ndap(arr) for arr in ind_from_phase(self.phase, thickness)] return(None) -
- dm3file : dictionary-like