# nifti-snapshot
`nifti-snapshot` is a tool to quickly capture nifti image as a `png` or
`jpeg` figures.
```sh
$ pip install nifti_snapshot
```
For full documentation: [Here](https://nifti-snapshot.readthedocs.io/en/latest/)
## TBSS figures
### From commandline
#### Snapshot of an `tbss_fill` image
```sh
fw=tbss_FW_tfce_corrp_tstat2_filled.nii.gz
./nifti_snapshot \
--input ${fw} \
--tbss \
--output_file cli_test_fw.png \
--cmap "Blues_r" \
--title "Significant changes in FW in group A" \
--cbar_title 'Increased FW'
```
<br>
#### Snapshot of two `tbss_fill` images with overlap highlight
```shell
fa=tbss_FA_tfce_corrp_tstat1_filled.nii.gz
fat=tbss_FAt_tfce_corrp_tstat1_filled.nii.gz
./nifti_snapshot \
--input ${fa} ${fat} \
--tbss \
--output_file cli_test.png \
--cmap "Blues_r" "autumn" \
--title "Significant changes in FA and FAt in group A" \
--cbar_title 'Reduced' 'Reduced FAt' 'Overlap' \
--overlap \
--overlap_cmap "summer" \
--overlap_alpha 0.8
```
---
### From python
#### Snapshot of an `tbss_fill` image
```py
from nifti_snapshot import nifti_snapshot
fw = 'tbss_FA_tfce_corrp_tstat1_filled.nii.gz'
fw_color = 'Blues_r'
tbssFigure = nifti_snapshot.TbssFigure(
image_files=[fw],
output_file='docs/fw_example.png',
cmap_list=[fw_color],
cbar_titles=['Increased FW'],
alpha_list=[0.8],
title='Increased Freewater in group A',
cbar_x=0.35, cbar_width=0.3)
tbssFigure.create_figure_one_map()
```
#### Snapshot of two `tbss_fill` images with overlap highlight
```py
from nifti_snapshot import nifti_snapshot
fa = 'tbss_FA_tfce_corrp_tstat1_filled.nii.gz'
fat = 'tbss_FAt_tfce_corrp_tstat1_filled.nii.gz'
fa_color_1 = 'Blues_r'
fa_color_2 = 'autumn'
fa_color_overlap = 'summer'
tbssFigure = nifti_snapshot.TbssFigure(
image_files=[fa, fat],
output_file='docs/fa_fat_example.png',
cmap_list=[fa_color_1, fa_color_2],
overlap_cmap=fa_color_overlap,
cbar_titles=[
'Reduced FA',
'Reduced FAt',
'Overlap'],
alpha_list=[1, 1, 0.8],
title='Significant changes in FA and FAt in group A')
tbssFigure.create_figure_two_maps_and_overlap()
```
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"description": " \n\n# nifti-snapshot\n\n`nifti-snapshot` is a tool to quickly capture nifti image as a `png` or\n`jpeg` figures.\n\n\n```sh\n$ pip install nifti_snapshot\n```\n\nFor full documentation: [Here](https://nifti-snapshot.readthedocs.io/en/latest/)\n\n\n## TBSS figures\n\n### From commandline\n\n#### Snapshot of an `tbss_fill` image\n\n```sh\nfw=tbss_FW_tfce_corrp_tstat2_filled.nii.gz\n\n./nifti_snapshot \\\n --input ${fw} \\\n --tbss \\\n --output_file cli_test_fw.png \\\n --cmap \"Blues_r\" \\\n --title \"Significant changes in FW in group A\" \\\n --cbar_title 'Increased FW' \n```\n\n\n\n\n<br>\n\n#### Snapshot of two `tbss_fill` images with overlap highlight\n\n```shell\nfa=tbss_FA_tfce_corrp_tstat1_filled.nii.gz\nfat=tbss_FAt_tfce_corrp_tstat1_filled.nii.gz\n\n./nifti_snapshot \\\n --input ${fa} ${fat} \\\n --tbss \\\n --output_file cli_test.png \\\n --cmap \"Blues_r\" \"autumn\" \\\n --title \"Significant changes in FA and FAt in group A\" \\\n --cbar_title 'Reduced' 'Reduced FAt' 'Overlap' \\\n --overlap \\\n --overlap_cmap \"summer\" \\\n --overlap_alpha 0.8\n```\n\n\n\n\n\n---\n\n\n### From python\n\n#### Snapshot of an `tbss_fill` image\n\n```py\nfrom nifti_snapshot import nifti_snapshot\nfw = 'tbss_FA_tfce_corrp_tstat1_filled.nii.gz'\nfw_color = 'Blues_r'\n\ntbssFigure = nifti_snapshot.TbssFigure(\n image_files=[fw],\n output_file='docs/fw_example.png',\n cmap_list=[fw_color],\n cbar_titles=['Increased FW'],\n alpha_list=[0.8],\n title='Increased Freewater in group A',\n cbar_x=0.35, cbar_width=0.3)\ntbssFigure.create_figure_one_map()\n```\n\n#### Snapshot of two `tbss_fill` images with overlap highlight\n\n```py\nfrom nifti_snapshot import nifti_snapshot\nfa = 'tbss_FA_tfce_corrp_tstat1_filled.nii.gz'\nfat = 'tbss_FAt_tfce_corrp_tstat1_filled.nii.gz'\n\nfa_color_1 = 'Blues_r'\nfa_color_2 = 'autumn'\nfa_color_overlap = 'summer'\n\ntbssFigure = nifti_snapshot.TbssFigure(\n image_files=[fa, fat],\n output_file='docs/fa_fat_example.png',\n cmap_list=[fa_color_1, fa_color_2],\n overlap_cmap=fa_color_overlap,\n cbar_titles=[\n 'Reduced FA',\n 'Reduced FAt',\n 'Overlap'],\n alpha_list=[1, 1, 0.8],\n title='Significant changes in FA and FAt in group A')\ntbssFigure.create_figure_two_maps_and_overlap()\n```\n\n\n\n\n",
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