Usage
AFMReader currently obtains the raw image data from your selected channel, and the
pixel-to-nanometre scaling value (pixels are assumed to be square) for the physical dimensions of the image for
all formats except the .topostats format. The .topostats metadata will contain that from the processing steps from
TopoStats.
If you wish to process AFM images supported by AFMReader it is recommend you use
TopoStats to do so, however the library can be used on its own if you wish to
integrate it into your workflow.
Supported file formats
| File format | Description |
|---|---|
.asd |
High-speed AFM |
.ibw |
WaveMetrics |
.spm |
Bruker's Format |
.jpk |
Bruker |
.topostats |
TopoStats |
.gwy |
Gwydion |
Support for the following additional formats is planned. Some of these are already supported in TopoStats and are awaiting refactoring to move their functionality into AFMReader these are denoted in bold below.
| File format | Description | Status |
|---|---|---|
.nhf |
Nanosurf | To Be Implemented. |
.aris |
Imaris Oxford Instruments | To Be Implemented. |
.tiff |
Park Systems | To Be Implemented. |
Configuration
A default configuration is included in the package which contains options for loading different file formats. This is a
YAML file with keys for each file type and the relevant key/value pair nested within. The table
below details the current configuration options. If loading a file format supports a custom configuration file then it
can be specified with the config_path parameter which should point to the location of the file.
| File format | Keys | Default value |
|---|---|---|
jpk |
n_slots |
32896 |
default_slot |
32897 |
|
first_slot_tag |
32912 |
|
first_scaling_type |
32931 |
|
first_scaling_name |
32932 |
|
first_offset_name |
32933 |
|
channel_name |
32848 |
|
trace_retrace |
32849 |
|
grid_ulength |
32834 |
|
grid_vlength |
32835 |
|
grid_ilength |
32838 |
|
grid_jlength |
32839 |
|
slot_size |
48 |
.topostats
You can open .topostats files using the load_topostats function. Just pass in the path to the file.
from AFMReader.topostats import load_topostats
image, pixel_to_nanometre_scaling_factor, metadata = load_topostats(file_path="./my_topostats_file.topostats")
.spm
You can open .spm files using the load_spm function. Just pass in the path to the file and the
channel name that you want to use. (If in doubt use one of the following: "Height", "ZSensor",
"Height Sensor").
from AFMReader.spm import load_spm
image, pixel_to_nanometre_scaling_factor = load_spm(file_path="./my_spm_file.spm", channel="Height")
.gwy
You can open .gwy files using the load_gwy function. Just pass in the path to the file and the
channel name that you want to use. (If in doubt use one one of the following: "Height", "ZSensor",
"Height Sensor").
from AFMReader.gwy import load_gwy
image, pixel_to_nanometre_scaling_factor = load_gwy(file_path="./my_gwy_file.gwy", channel="Height")
.asd
You can open .asd files using the load_asd function. Just pass in the path to the file and the channel name that you
want to use. (If in doubt use the "TP" topography channel).
Note: For .asd files, there seem to only ever be two channels in one file. "TP" (topography) is the main one you
will want to use unless you know you specifically want something else.
Other channels: "ER" - Error, "PH" - Phase
from AFMReader.asd import load_asd
frames, pixel_to_nanometre_scaling_factor, metadata = load_asd(file_path="./my_asd_file.asd", channel="TP")
.ibw
You can open .ibw files using the load_ibw function. Just pass in the path to the file
and the channel name that you want to use. (If in doubt, use HeightTracee (yes, with the
extra 'e'), ZSensorTrace, or ZSensor).
from AFMReader.ibw import load_ibw
image, pixel_to_nanometre_scaling_factor = load_ibw(file_path="./my_ibw_file.ibw", channel="HeightTrace")
.jpk
You can open .jpk files using the load_jpk function. Just pass in the path
to the file and the channel name you want to use. (If in doubt, use height_trace or measuredHeight_trace).