Datacube
load
¤
Create a 3D array (X and Y are the dimensions of the sample and Z dimension is the number of elements/emission lines taken into account for the classification).
Stack the information contained in the elemental files given ranked according to the spreasheet ranking.
If normalization is asked or if the elemental map is an image file, data in the array are between 0 and 100.
Three types of elemental files are accepted
-
Imges (.bmp of .tif), which are RGB files : each pixel contains 3 values between 0 and 255. The rgb is put into greyscale calculated by the norm 2.
-
Textfile (.txt), which is already the elemental array where the values are the number of counts.
-
Raw file (.rpl), wich is the datacube containing all the spectra for every pixel. The hyperspy library is used to extract the emission lines corresponding to the wanted elements.
Textfiles and raw files can be normalized or not, the spreadsheet must be written according to that.
The function also creates a dictionnary containing the Z position of the element in the 3D array created.
2 class files created in that function.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
prefix |
str
|
Common name between files. |
required |
suffix |
str
|
Extension name of the files. |
required |
normalization |
bool
|
If data are normalized between 0 and 100. |
True
|
element_list |
List[str]
|
User can specify list elements to be taken, or let the program finds all data in corresponding to given prefix name. |
None
|
Raises:
| Type | Description |
|---|---|
TypeError
|
If given extension is not accepted by the program. |
load_images
¤
Images Data loader.
Low-level function for data loading.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
file_list |
List[str]
|
List of images files to load. |
required |
prefix |
str
|
Common name between files. |
required |
suffix |
str
|
Extension name of the files. |
required |
Returns:
| Type | Description |
|---|---|
MultiCube
|
Marcia MultiCube Objects. |
MultiCube
|
MultiCube means data channels are discrete and not continuous. |
load_textfile
¤
Text Data Loader.
Low-level function for data loading.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
file_list |
List[str]
|
List of images files to load. |
required |
prefix |
str
|
Common name between files. |
required |
suffix |
str
|
Extension name of the files. |
required |
normalization |
bool
|
If data are normalized between 0 and 100. |
True
|
Returns:
| Type | Description |
|---|---|
MultiCube
|
Marcia MultiCube Objects. |
MultiCube
|
MultiCube means data channels are discrete and not continuous. |
load_hypermap
¤
Raw HyperCube Data Loader.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
prefix |
str
|
Name of file. |
required |
suffix |
str
|
Extension name of the file. |
required |
name |
str
|
Physical measure of channel |
'E'
|
units |
str
|
Unit of physical measure. Defaults to 'keV'. |
'keV'
|
scale |
float
|
Scale realationship betwen channel and physical measure. |
0.01
|
offset |
float
|
Scale offset between channel and physcial measure. |
-0.97
|
Returns:
| Type | Description |
|---|---|
HyperCube
|
Marcia HyperCube Object. |
HyperCube
|
HyperCube means data channels are continuous. |
save
¤
save_cube_inside_mask
¤
Recreates raw datacube containing data only in the wanted element.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
data_cube |
DataCube
|
Marcia DataCube Object. |
required |
mineral |
str
|
Name of the wanted element (eg: 'Galene') |
required |
Raises:
| Type | Description |
|---|---|
FileNotFoundError
|
If raw data cube is not in folder. |
save_cube_outside_mask
¤
Recreates a raw datacube containing data that are not in the specified element.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
data_cube |
DataCube
|
Marcia DataCube Object. |
required |
mineral |
str
|
Name of the wanted element (eg: 'Galene') |
required |
Raises:
| Type | Description |
|---|---|
FileNotFoundError
|
If raw data cube is not in folder. |
save_mask_spectrum
¤
Save mean spectrum of a given mask as a .txt file.
- First column is channel.
- Second column is counts.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
data_cube |
DataCube
|
Marcia DataCube Object. |
required |
mask |
str
|
Name of the wanted mask (eg: 'Galene'). |
required |
Raises:
| Type | Description |
|---|---|
FileNotFoundError
|
If raw data cube is not in folder. |