Reading a Nion File with ScopeReader¶
Gerd Duscher
12/05/2020
This document is a simple example of how to read Nion Files into the sidpy dataformat
UNDER CONSTRUCTION
Introduction¶
Swift from Nion runs on all of Nion’s STEMs for acquisition. We read and plot such files here.
Import all necessary packages¶
There are a few setup procedures that need to be followed before any code is written. In this step, we simply load a few python packages that will be necessary in the later steps.
[5]:
%pylab notebook
%gui qt
import os
import sys
from sidpy.io.interface_utils import openfile_dialog
sys.path.append('../')
from SciFiReaders import NionReader
import SciFiReaders
print('SciFiReaders version: ', SciFiReaders.__version__)
import sidpy
print('sidpy version: ', sidpy.__version__)
Populating the interactive namespace from numpy and matplotlib
SciFiReaders version: 0.0.1
sidpy version: 0.0.5
Open a file dialog¶
Here we select the name of the file to open. We will be using the sidpy interface to do that.
The openfile_dialog will open QT file dialog to select a file.
For examples go to the example_data directory in the original folder of this notebook.
Note.: in some operating systems the window will not show up on top, look in your task bar.
[2]:
file_name = openfile_dialog()
print(file_name)
/home/o2d/Dropbox (ORNL)/TEM data/2021/2021-04-16-Cr-graphene-US100-60kV-60pA/Nion Swift Project 20210416 Data/2021/04/16/20210416-142215/data_0UEJQVTQ9X8OQYF8HJO70C8CB.ndata
Catch a bad selection or cancelling of file selection¶
[3]:
if len(file_name) < 3:
print('No valid file selected')
else:
path, base_file_name = os.path.split(file_name)
basename, extension = os.path.splitext(base_file_name)
if extension not in ['.ndata', '.h5']:
print('File not supported')
Read file¶
We use the ScopeReader to read the file into a sidpy dataset. All metadata (absolutely everything) is saved in the original_metadata attribute of the sidpy Dataset. If the selected file is not a Nion File you get a TypeError.
[6]:
nion_reader = NionReader(file_name)
dataset = nion_reader.read()
print(dataset)
dataset
sidpy.Dataset of type IMAGE with:
dask.array<generic, shape=(256, 256), dtype=float32, chunksize=(256, 256), chunktype=numpy.ndarray>
data contains: intensity (counts)
and Dimensions:
y: distance (nm) of size (256,)
x: distance (nm) of size (256,)
[6]:
|
Plot File¶
Only one command is necessary to plot the file.
[7]:
dataset.plot()
Original Metadata¶
Digital micrograph stores a lot of metadata in the file and we read all of them and store that information in the original_metadata.
[8]:
dataset.view_original_metadata()
type : data-item
uuid : 1242c2e8-618b-49c2-aea7-f5a5dbd03373
created : 2021-04-16T20:40:19.416463
is_sequence : False
intensity_calibration :
offset : 0.0
scale : 1.0
units :
dimensional_calibrations : [{'offset': -10.0, 'scale': 0.078125, 'units': 'nm'}, {'offset': -10.0, 'scale': 0.078125, 'units': 'nm'}]
timezone : America/New_York
timezone_offset : -0400
metadata :
instrument :
high_tension : 60000.0
defocus : 3.3413595086161986e-10
ImageScanned :
C1 ConstW : 0.535
C10 : 3.3413595086161986e-10
C10Control : 0.0
C12.a : 7.790575877604827e-09
C12.b : -9.344480956695125e-09
C2 ConstW : 0.759
C21.a : 2.3036487004760242e-07
C21.b : 1.580289523538976e-07
C23.a : 2.8574413811668664e-08
C23.b : 2.6551966593848706e-08
C3 ConstW : 0.971829
C30 : 1.986602299690654e-06
C32.a : 6.5178947510754046e-06
C32.b : 9.143814019988201e-06
C34.a : 3.281084172769262e-06
C34.b : 2.3774745854848426e-06
C41.a : -0.0003642179172182993
C41.b : -0.0002498513591704886
C43.a : -6.776627974180181e-05
C43.b : -6.296990054644458e-05
C45.a : -0.00026451435339213097
C45.b : -6.462188328094359e-05
C50 : -0.0052123977838471015
C52.a : -0.011348718258983872
C52.b : -0.002997953401518279
C54.a : -0.005022485544683429
C54.b : -0.0015520939749976963
C56.a : 0.0010483179923364597
C56.b : -0.00016883886847779785
EHT : 60000.0
PMTBF_gain : 4096000.0
PMTDF_gain : 1024000.0
SShft.sx : -0.00012910587277402402
SShft.sy : -0.00019696069461356278
SShftZ : -3.4789550834968264e-05
StageCoordU : 0.0004952773115228157
StageCoordV : 0.0017437740677182785
StageOutA : -3.5118041570771e-08
StageOutB : 3.114038584183673e-08
StageOutX : -0.00012910587277402402
StageOutY : -0.00019696069461356278
StageOutZ : -3.4789550834968264e-05
PL1 : 0.54036
PL2 : 0.0
PL3 : 0.8263
PL4 : 1.241
scan :
hardware_source_id : superscan
hardware_source_name : SuperScan
scan_id : 02a1025e-d701-415f-ac1e-7472c803906a
center_x_nm : 0.0
center_y_nm : 0.0
fov_nm : 20.0
rotation : 0.21293016874330817
rotation_deg : 12.199999999999998
scan_context_size : [256, 256]
subscan_fractional_size : [1.0, 1.0]
scan_size : [256, 256]
subscan_fractional_center : [0.5, 0.5]
scan_device_parameters :
size : [256, 256]
center_nm : [0.0, 0.0]
pixel_time_us : 750
fov_nm : 20.0
rotation_rad : 0.21293016874330817
ac_line_sync : False
ac_frame_sync : False
flyback_time_us : 300
external_clock_mode : 1
external_clock_wait_time_ms : 20000
external_scan_mode : 0
external_scan_ratio : 1.0
subscan_pixel_size : [256, 256]
subscan_fractional_size : [1.0, 1.0]
subscan_fractional_center : [0.5, 0.5]
subscan_rotation : 0.0
scan_id : 02a1025e-d701-415f-ac1e-7472c803906a
section_rect : [[0, 0], [256, 256]]
data_shape_override : [256, 256]
state_override : complete
top_left_override : [0, 0]
scan_device_properties :
ac_line_sync : 2.0
center_x_nm : 0.0
center_y_nm : 0.0
flyback_time_us : 1500.0
fov_nm : 20.0
line_time_us : 193500.0
pixel_time_us : 750.0
pixels_x : 256.0
pixels_y : 256.0
requested_pixel_time_us : 750.000006519258
rotation_deg : 12.2
rotation_rad : 0.212930168743308
mag_boards :
MagBoard 0 DAC 0 : 0.0
MagBoard 0 DAC 1 : 0.0
MagBoard 0 DAC 10 : 40403.0
MagBoard 0 DAC 11 : 16709.0
MagBoard 0 DAC 2 : 0.0
MagBoard 0 DAC 3 : 0.0
MagBoard 0 DAC 4 : 40433.0
MagBoard 0 DAC 5 : 17084.0
MagBoard 0 DAC 6 : 1434.0
MagBoard 0 DAC 7 : 64215.0
MagBoard 0 DAC 8 : 64586.0
MagBoard 0 DAC 9 : 866.0
MagBoard 0 Relay : 32.0
MagBoard 1 DAC 0 : 0.0
MagBoard 1 DAC 1 : 0.0
MagBoard 1 DAC 10 : 0.0
MagBoard 1 DAC 11 : 0.0
MagBoard 1 DAC 2 : 0.0
MagBoard 1 DAC 3 : 0.0
MagBoard 1 DAC 4 : 0.0
MagBoard 1 DAC 5 : 0.0
MagBoard 1 DAC 6 : 0.0
MagBoard 1 DAC 7 : 0.0
MagBoard 1 DAC 8 : 0.0
MagBoard 1 DAC 9 : 0.0
MagBoard 1 Relay : 32.0
valid_rows : 256
hardware_source :
hardware_source_id : superscan
hardware_source_name : SuperScan
exposure : 49.152
frame_index : 0
channel_id : a
channel_name : a
pixel_time_us : 750.0
line_time_us : 193500.0
valid_rows : 256
channel_index : 0
reference_key : superscan_a
view_id : fd80be9e-5016-4b24-9aa3-6600cc176395
title : Spectrum Image (a)
session_id : 20210416-142215
session :
site : Oak Ridge National Laboratory
instrument : NION UltraSTEM 100
task :
microscopist :
sample :
sample_area :
category : persistent
version : 13
modified : 2021-04-16T20:40:31.628236
data_shape : [256, 256]
data_dtype : float32
collection_dimension_count : 0
datum_dimension_count : 2
data_modified : 2021-04-16T20:40:31.399368
[ ]: