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Update documentation, quick start tutorial

feature/load_slices
Ruben Verweij 7 years ago
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416f4f69fc
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      docs
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      sphinx/conf.py
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      sphinx/nd2reader.rst
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      sphinx/tutorial.md

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docs

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Subproject commit 6e17cadb9d79143c4e41ababeb309d4e88f9038b
Subproject commit f4e4a67ac24cf12b3c0b6e5aae0dbb2f3497bb73

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sphinx/conf.py View File

@ -44,9 +44,9 @@ author = 'Ruben Verweij'
# built documents.
#
# The short X.Y version.
version = ''
version = '3.0.0'
# The full version, including alpha/beta/rc tags.
release = ''
release = '3.0.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.


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sphinx/nd2reader.rst View File

@ -55,7 +55,7 @@ nd2reader.exceptions module
:undoc-members:
:show-inheritance:
nd2reader.exceptions artificial
nd2reader.artificial module
-------------------------------
.. automodule:: nd2reader.artificial


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sphinx/tutorial.md View File

@ -23,4 +23,35 @@ with ND2Reader('my_directory/example.nd2') as images:
plt.imshow(images[0])
```
After opening the file, all `pims` features are supported. Please refer to the [pims documentation](http://soft-matter.github.io/pims/).
After opening the file, all `pims` features are supported. Please refer to the [pims documentation](http://soft-matter.github.io/pims/).
### ND2 metadata
The ND2 file contains various metadata, such as acquisition information,
regions of interest and custom user comments. Most of this metadata is parsed
and available in dictionary form. For example:
```python
from nd2reader import ND2Reader
with ND2Reader('my_directory/example.nd2') as images:
# width and height of the image
print('%d x %d px' % (images.metadata['width'], images.metadata['height']))
```
All metadata properties are:
* `width`: the width of the image in pixels
* `height`: the height of the image in pixels
* `date`: the date the image was taken
* `fields_of_view`: the fields of view in the image
* `frames`: a list of all frame numbers
* `z_levels`: the z levels in the image
* `total_images_per_channel`: the number of images per color channel
* `channels`: the color channels
* `pixel_microns`: the amount of microns per pixel
* `rois`: the regions of interest (ROIs) defined by the user
* `experiment`: information about the nature and timings of the ND experiment

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