[doc] fix tutorials. Now EDFTomoScan.projections only return the none...

[doc] fix tutorials. Now EDFTomoScan.projections only return the none alignment projections. And there is only 20 projections of those

[doc] fix tutorials. Now EDFTomoScan.projections only return the none...
f54423eb · payno · d0563409 · f54423eb
Commit f54423eb authored 4 years ago by payno
--- a/doc/tutorials/edf_scan.ipynb
+++ b/doc/tutorials/edf_scan.ipynb
@@ -166,7 +166,7 @@
   ],
   "source": [
    "from silx.io.utils import get_data\n",
-    "frame_28_data = get_data(scan.projections[28])\n",
+    "frame_18_data = get_data(scan.projections[18])\n",
    "# imshow(frame_28_data)"
   ]
  },

 %% Cell type:markdown id: tags:

 # Read data from an EDF acquisition


 To create a 'Scan' object from EDF you have to use the :class:`EDFTomoScan` class and provide the path to the acquisition

 WARNING: Browsing EDF files is based on several convention at ESRF.
             The most important one is that the acquisition 'identification' - which is the folder name is repeated in the file names.
             For example if we have an acquisition names 'acq_0005' we expect edf file prefix to be 'acq_0005' too.

 WARNING: The :class:`EDFTomoScan` has been tested on EDF single frame files. It wouldn't be surprising if it fails on EDF multiple frames files.


 %% Cell type:code id: tags:

 ``` python
 # %pylab # to use imshow uncomment
 ```

 %% Output

    Using matplotlib backend: Qt5Agg
    Populating the interactive namespace from numpy and matplotlib

 %% Cell type:markdown id: tags:

 ## Get a simple dataset for test (this dataset is a pure noise)

 %% Cell type:code id: tags:

 ``` python
 from tomoscan.test.utils import UtilsTest
 import os

 data_dir = UtilsTest.getDataset('test10')
 ```

 %% Cell type:markdown id: tags:

 ## create an instance of `EDFTomoScan`

 `EDFTomoScan` implements the TomoScanBase interface.
 This allow you to have a common API for accessing data from EDF or HDF5 regardless of the type of acquisition.

 %% Cell type:code id: tags:

 ``` python
 from tomoscan.esrf.edfscan import EDFTomoScan
 scan = EDFTomoScan(scan=data_dir)
 ```

 %% Cell type:markdown id: tags:

 Then from it you can access several information

 %% Cell type:markdown id: tags:

 ### projections

 %% Cell type:code id: tags:

 ``` python
 scan.projections
 ```

 %% Output

    {3: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100003.edf', data_path=None, data_slice=[0]),
     27: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100027.edf', data_path=None, data_slice=[0]),
     0: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100000.edf', data_path=None, data_slice=[0]),
     31: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100031.edf', data_path=None, data_slice=[0]),
     20: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100020.edf', data_path=None, data_slice=[0]),
     25: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100025.edf', data_path=None, data_slice=[0]),
     7: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100007.edf', data_path=None, data_slice=[0]),
     19: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100019.edf', data_path=None, data_slice=[0]),
     8: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100008.edf', data_path=None, data_slice=[0]),
     5: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100005.edf', data_path=None, data_slice=[0]),
     4: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100004.edf', data_path=None, data_slice=[0]),
     22: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100022.edf', data_path=None, data_slice=[0]),
     26: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100026.edf', data_path=None, data_slice=[0]),
     32: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100032.edf', data_path=None, data_slice=[0]),
     14: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100014.edf', data_path=None, data_slice=[0]),
     18: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100018.edf', data_path=None, data_slice=[0]),
     30: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100030.edf', data_path=None, data_slice=[0]),
     2: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100002.edf', data_path=None, data_slice=[0]),
     16: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100016.edf', data_path=None, data_slice=[0]),
     15: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100015.edf', data_path=None, data_slice=[0]),
     23: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100023.edf', data_path=None, data_slice=[0]),
     11: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100011.edf', data_path=None, data_slice=[0]),
     13: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100013.edf', data_path=None, data_slice=[0]),
     1: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100001.edf', data_path=None, data_slice=[0]),
     17: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100017.edf', data_path=None, data_slice=[0]),
     24: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100024.edf', data_path=None, data_slice=[0]),
     12: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100012.edf', data_path=None, data_slice=[0]),
     9: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100009.edf', data_path=None, data_slice=[0]),
     29: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100029.edf', data_path=None, data_slice=[0]),
     21: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100021.edf', data_path=None, data_slice=[0]),
     28: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100028.edf', data_path=None, data_slice=[0]),
     10: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100010.edf', data_path=None, data_slice=[0]),
     6: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/test100006.edf', data_path=None, data_slice=[0])}

 %% Cell type:markdown id: tags:

 This return a dictionnary of projection index and DataUrl.
 You can access the data using `silx.io.utils.get_data function`

 %% Cell type:code id: tags:

 ``` python
 from silx.io.utils import get_data
-frame_28_data = get_data(scan.projections[28])
+frame_18_data = get_data(scan.projections[18])
 # imshow(frame_28_data)
 ```

 %% Output

    <matplotlib.image.AxesImage at 0x7f5ce5bbcc88>

 %% Cell type:markdown id: tags:

 ### darks

 %% Cell type:code id: tags:

 ``` python
 scan.darks
 ```

 %% Output

    {}

 %% Cell type:markdown id: tags:

 ### flats

 %% Cell type:code id: tags:

 ``` python
 scan.flats
 ```

 %% Output

    {20: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/refHST0020.edf', data_path=None, data_slice=[0]),
     10: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/refHST0010.edf', data_path=None, data_slice=[0]),
     0: DataUrl(valid=True, scheme='fabio', file_path='/home/payno/dev/tomo/tomoscan/tomoscan/test/test10/refHST0000.edf', data_path=None, data_slice=[0])}

 %% Cell type:markdown id: tags:

 ### energy (in keV)

 %% Cell type:code id: tags:

 ``` python
 scan.energy
 ```

 %% Output

    19.0

 %% Cell type:markdown id: tags:

 ### pixel size (in )

 %% Cell type:code id: tags:

 ``` python
 scan.get_pixel_size(unit='cm')
 ```

 %% Output

    0.00030199999999999997

 %% Cell type:markdown id: tags:

 There is more information that you can access, to get them all please have a look on the [TomwerScanBase API](https://tomotools.gitlab-pages.esrf.fr/tomoscan/modules/scanbase.html#tomoscan.scanbase.TomoScanBase) and [EDFTomoScan API](https://tomotools.gitlab-pages.esrf.fr/tomoscan/modules/esrf.html#tomoscan.esrf.edfscan.EDFTomoScan).