pyemaps 0.3.4

Python Modules for Transmission Electron Diffraction Simulations

Introducing pyemaps

1. Overview

2. Requirements

3. Installation

4. Basic Usage

5. Getting Started

6. Visualization

7. License

Overview ↩

pyemaps package is a collection of python modules and libraries designed for transmission electron diffraction simulations and related crystallographic calculations. Main features include:

Crystal : crystal data module, classes and methods loading crystal data from various sources, including diffraction patterns generation based on the crystal data and microscope and sample control parameters

DP : kinematic diffraction python class. It encapsulates diffraction pattern data generated by the Crystal class instance and diffraction pattern visualization methods such as plotting Kikuchi and HOLZ lines, and diffraction spots or disks and their indices.

pyemaps is based on the proprietary Fortran applications released as backend of cloudEMAPS2.0.

Future releases planned include:

Bloch : dynamic Bloch wave simulation.

Check EMlab Solution, Inc. for updates and releases. We welcome comments and suggestions from our user community. For reporting any issues and requesting pyemaps improvements, or sharing scripts using pyemaps, please go to our support page.

If you benefit from pyemaps in your microscopy and crystallography research and education, go to PayPal to donate. Your generous donations keep us in the business of providing free software to the communities.

Requirements ↩

• Python: Version >= 3.6

• Operating Systems: Windows

Linux support planned in future releases, stay tuned.

Installation ↩

(.venv) $ pip install pyemaps

where .venv is the python virtual environment

PYEMAPS_CRYSTALS environment variable is optional. But setting it to a directory where all custom

crystal data files are located provides central location for organizing your own crystal data. pyemaps also searches this directory for your crystal data.

    PYEMAPS_CRYSTALS=<local directory>

Basic Usage ↩

from pyemaps import Crystal

from pyemaps import DP

Getting Started ↩

Run the following on command line, after above successful installation:

python sample.py

where sample.py is as follows:

#import Crystal class from pyemaps as cryst

from pyemaps import Crystal as cryst

# create a crystal class instance and load it with builtin silicon data

si = cryst.from_builtin('silicon')



# generate diffraction on the crystal instance with all default controls

# parameters

si_dp = si.gen_diffPattern()

#plot and show the diffraction pattern using pyemaps built-in plot function

si_dp.plot()

The alternative to run the above without creating sample.py:

python -m pyemaps --sample (-s)

The diffraction plot is generated with silicon crystal data built in the package:

crystal Silicon: dw = iso

cell 5.4307 5.4307 5.4307 90 90 90

atom si 0.125 0.125 0.125 0.4668 1.00

spg 227 2

and default electron microscope and sample control parameters:

zone axis: (0,0,1)

microscope mode: normal

microscope camera length : 1000 mm

microscope voltage: 200 kv

sample tilt: (0.0,0.0)

sample offset: (0.0,0.0)

spot size: 0.05 Å

To see all crystal names with builtin data, call:

cryst.list_all_builtin_crystals()

where cryst is imported pyemaps Crystal class

To use a crystal data not in built-in database in above format (as xtl format), replace the code in sample.py:

si = cryst.from_builtin('silicon')

with:

si = cryst.from_xtl(fn)

where fn is a crystal data file name.

Note: pyemaps searches for fn if the full path is provided. Otherwise, it will look up the file in current working directory or in the directory set by PYEMAPS_CRYSTALS environment variable. In latter cases, fn is just the file name without path.

Checking pyemaps version and displaying copyright information:

python -m pyemaps -c (--copyright)

python -m pyemaps -v (--version)

Visualization ↩

In addition to Python's matplotlib for displaying diffraction patterns generated by pyemaps as shown above, DigitalMicrography (referred as DM here) is another option. The python script support in DM can realize the diffraction patterns from pyemaps with its line and circle annotations as demonstrated below:

import numpy as np

import DigitalMicrograph as DM

from pyemaps import XMAX, YMAX

#----diffraction patterns generated by these bounds

#   [-XMAX, XMAX, -YMAX, YMAX]

#    screen size multiplier

mult = 4

#simple diffraction mode lookup

DIFF_MODE = ('Normal', 'CBED')

#------Diffraction modes-------

#       1 - normal

#       2 - CBED

def SetCommonProp(comp):

    comp.SetResizable(False)

    comp.SetMovable(False)

    comp.SetDeletable(False)

    

def show_diffract(dp, md=1, name = 'Diamond'):   

    shape = (2*XMAX*mult,2*YMAX*mult)

    dif_raw = np.ones((shape), dtype = np.float32)

    dif_raw[:,:] = 255.0

    dm_dif_img = DM.CreateImage(dif_raw)

    dif_img = dm_dif_img.ShowImage()

    dif_img_disp = dm_dif_img.GetImageDisplay(0)

    

    if md <1 or md > 2:

        print(f'diffraction mode provided {md} not supported')

        return 1

    

    img_title = str(f'Kinematic Diffraction Simulation:  {name} in {DIFF_MODE[md-1]} Mode')

    dm_dif_img.SetName(img_title)    

    #xs,ys = diff_dict['bounds'] # not used

    num_klines = dp.nklines

    if num_klines > 0:

        klines = dp.klines

        for kl in klines:        

            x1, y1, x2, y2 = kl             

            xx1, yy1, = (x1 + XMAX)*mult,(y1 + YMAX)*mult 

            xx2, yy2  = (x2 + XMAX)*mult,(y2 + YMAX)*mult            

            kline = dif_img_disp.AddNewComponent(2, xx1, yy1, xx2, yy2)            

            SetCommonProp(kline)

            kline.SetForegroundColor(0.7, 0.7, 0.7) #grey

            kline.SetBackgroundColor(0.2,0.2,0.5)# dark blue

    num_disks = dp.ndisks

    if num_disks > 0:

        disks = dp.disks

        for d in disks:

            x1, y1, r, i1, i2, i3 = d

            xx, yy, rr = (x1 + XMAX)*mult, (y1 + YMAX)*mult, r*mult                         

            idx = '{:d} {:d} {:d}'.format(i1,i2,i3)            

            disk = dif_img_disp.AddNewComponent(6, xx-rr, yy-rr, xx+rr, yy+rr)

            

            SetCommonProp(disk)

            disk.SetForegroundColor(0.0,0.0,1.0) # blue

            disk.SetBackgroundColor(0.5,0.5,0.75)# dark blue

            if md == 1:

                disk.SetFillMode(1)

            else:

                disk.SetFillMode(2)        

            indxannot0 = DM.NewTextAnnotation(0, 0, idx, 10)            

            t, l, b, r = indxannot0.GetRect()

            w = r-l

            h = b-t            

            nl = xx - ( w / 2)

            nr = xx + ( w / 2)

            nt = yy -rr - h if md ==1 else yy - (h / 2)

            nb = yy + rr + h if md == 1 else yy + (h / 2)            

            indxannot = DM.NewTextAnnotation(nl, nt, idx, 10)            

            dif_img_disp.AddChildAtEnd(indxannot)

            SetCommonProp(indxannot)

            indxannot.SetForegroundColor(0.9,0,0) #light red

            indxannot.SetBackgroundColor(1,1,0.5)

            

    if md == 2:

        num_hlines = dp.nhlines

        if num_hlines > 0 :

            hlines = dp.hlines

            for hl in hlines:

                x1, y1, x2, y2 = hl

                xx1, yy1 = (x1 + XMAX)*mult, (y1 + YMAX)*mult 

                xx2, yy2 = (x2 + XMAX)*mult, (y2 + YMAX)*mult                

                hline = dif_img_disp.AddNewComponent(2, xx1, yy1, xx2, yy2)

                SetCommonProp(hline)

                hline.SetForegroundColor(0,0,0.8)

                hline.SetBackgroundColor(0.2,0.2,0.5)# dark blue                

    del dm_dif_img

    return 0              

      

def run_si_dm_sample():  

    from pyemaps import Crystal as cr

    #-----------load crystal data into a Crystal class object-----------------

    name = 'Silicon'

    si = cr.from_builtin(name)

    #-----------content of the crystal data-----------------------------------

    print(si)

    #-----------generate diffraction pattern in CBED mode---------------------

    si_dp_cbed = si.gen_diffPattern(mode = 2, dsize = 0.2)

    #-----------Plot the pattern in DM----------------------------------------

    show_diffract(si_dp_cbed, md = 2, name = name)



    #-----------generate diffraction pattern in normal mode-------------------

    si_dp = si.gen_diffPattern()

    #-----------content of the crystal data-----------------------------------

    show_diffract(si_dp, name = name)



run_si_dm_sample()

Other sample scripts designed for you to explore pyemaps are available in samples directory:

• si_tilt_normal.py: spot diffraction patterns generated with silicon crystal data, plotted with matplotlib pyplot module. The code also shows how a list of diffraction patterns are generated and displayed as one of electron microscope and sample control - tilt in x direction changes.

• si_tilt_cbed.py: The same as above with the diffraction mode set to CBED.

• pyplot_dm_si_diff.py: DM python script which generate and plot diffraction pattern for silicon crystal using matplotlib pyplot module

• pyplot_dm_si_diff_color.py: Similar to the above, the plot is done in color.

License ↩

pyemaps is distributed for electron diffraction and microscopy research, 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.

• pyemaps is for non-commercial use.

• pyemaps is free software 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. You should have received a copy of the GNU General Public License along with pyemaps. If not, see https://www.gnu.org/licenses/.

Contact [e-mail] for any questions regarding the license terms.