pict.binarize_nd - Compute a persistence diagram from an N-dimensional binary bitmap by using a cubical dilation-erosion filtration

```
python3 -m homcloud.pict.binarize_nd
[-h] [-V] [-T TYPE] [-m MODE] [-t THRESHOLD]
[--gt GT] [--lt LT] -o OUTPUT [-s] [-I]
[--metric METRIC] [-D] [-C] [-p PERIODIC]
[--mask MASK] [--algorithm ALGORITHM]
[-M SAVE_BOUNDARY_MAP] [--license]
[input [input ...]]
```

```
homcloud-pict-binarize-nd
```

This program computes a persistence diagram from an N-dimensional binary bitmap file by using a cubical dilation-erosion filtration.

The program accepts the following types of file formats:
`text2d`

, `text_nd`

, `picutre2d`

, `pictures3d`

and `npy`

.
If you want to know the details, please see INPUT FILE FORMAT section below.

The input bitmap data is binarized by a given threshold (-t). After that a dilation-erosion filtration is constructed and a persistnece diagram is computed and saved into the OUTPUT.

If you want to flip the roles of black pixels and white pixels, please use -m option.

By default manhattan distance is used. You can use other distances like euclidean or chebyshev by â€“metric option.

```
-h, --help show this help message and exit
-V, --version show program's version number and exit
-T TYPE, --type TYPE input data format
(text2d,text_nd(default),picture2d,pictures3d,npy)
-m MODE, --mode MODE the way to construct dipha complex (black-base|white-
base, default is black-base)
-t THRESHOLD, --threshold THRESHOLD
threshold for binarization (default: 128)
--gt GT lower threshold
--lt LT upper threshold
-o OUTPUT, --output OUTPUT
output complex file name
-s, --ensmall ensmall binarized picture
-I, --combine-index-map
combine the index map with the output filtration
--metric METRIC metric used to enlarge binarized image
(manhattan(default), euclidean, etc.)
-D, --convert-to-diagram
call dipha and directly convert to a diagram
-C, --cubical use explicit cubical filtration (slow)
-p PERIODIC, --periodic PERIODIC
periodic (example: 0,1,1 for y and z are periodic)
--mask MASK mask bitmap
--algorithm ALGORITHM
algorithm (dipha, phat-twist, phat-chunk-parallel)
-M SAVE_BOUNDARY_MAP, --save-boundary-map SAVE_BOUNDARY_MAP
save boundary map into idiagram file(only available
with phat-* algorithms, on/*off*)
--license show license and exit
```

The program accepts the following types of file formats:
`text2d`

, `text_nd`

, `picutre2d`

, `pictures3d`

and `npy`

.

2D pixel (floating point number) values represented by a text as follows:

```
x_11 x_12 ... x_1n
x_21 x_22 ... x_2n
: : :
x_m1 x_m2 ... x_mn
```

Each coefficient should be floating point numbers. These values are binarized by the threshold value given by -t option.

N-dimensional pixel (floating point number) values represented by a text as in the following format:

- First line represents the shape of data. For example, if the shape of your data
is 200x230x250, first line should be
`200 230 250`

. - The following lines are floating point number values in x-fastest direction
- A line starting with
`#`

is skipped as a comment - An empty line is also skipped.

An example is as follows:

```
# 4x3x2 3D voxel data
4 3 2
1 2 3 4
5 6 7 8
9 10 11 12
13 14 15 16
17 18 19 20
21 22 23 24
```

A gray scale PNG or TIFF file.

If the input file is 16bit grayscale file, the pixel value is normalized to the range of 0 .. 255.

Gray scale PNG or TIFF files. All picture sizes must be same. If not, an error occurs. All pictures are stacked in the commandline order.

If the input file is 16bit grayscale file, the pixel value is normalized to the range of 0 .. 255.

Numpy's npy file.

Please see https://docs.scipy.org/doc/numpy/neps/npy-format.html for details of this format.

If `-D`

option is given, the output file is not a boundary matrix data,
but a diagram data. In this case, a persistence diagram is computed
from the cubical filtration.
dipha's diagram file is written if `-I`

option is not given, and
indexed-diagram file (idiagarm) file is written if `-I`

option is given.

Now this program always should run `-D`

option. If `-D`

option is not given,
a warning message is shown.