Commit d703117e authored by syz's avatar syz
Browse files

Merge remote-tracking branch 'origin/cades_dev' into cades_dev_local

# Conflicts:
#	setup.py
parents 972bc0e5 f314598f
......@@ -8,7 +8,7 @@ pycroscopy |statusimage|
What is pycroscopy?
-------------------
pycroscopy is a `python <http://www.python.org/>`_ package for image processing and scientific analysis of imaging modalities such as multi-frequency scanning probe microscopy, scanning tunneling spectroscopy, x-ray diffraction microscopy, and transmission electron microscopy. pycroscopy uses a data-centric model wherein the raw data collected from the microscope, results fron analysis and processing routines are all written to standardized heirarchical data format (HDF5) files for traceability, reproducability, and prevenance.
pycroscopy is a `python <http://www.python.org/>`_ package for image processing and scientific analysis of imaging modalities such as multi-frequency scanning probe microscopy, scanning tunneling spectroscopy, x-ray diffraction microscopy, and transmission electron microscopy. pycroscopy uses a data-centric model wherein the raw data collected from the microscope, results from analysis and processing routines are all written to standardized hierarchical data format (HDF5) files for traceability, reproducibility, and provenance.
With `pycroscopy <https://pycroscopy.github.io/pycroscopy/>`_ we aim to:
1. Serve as a hub for collaboration across scientific domains (microscopists, material scientists, biologists...)
......@@ -87,9 +87,13 @@ Journal Papers using pycroscopy
 
4. `Direct Imaging of the Relaxation of Individual Ferroelectric Interfaces in a Tensile-Strained Film <http://onlinelibrary.wiley.com/doi/10.1002/aelm.201600508/full>`_ by L. Li et al.; Advanced Electronic Materials (2017), jupyter notebook `here 4 <http://nbviewer.jupyter.org/github/pycroscopy/pycroscopy/blob/master/jupyter_notebooks/BE_Processing.ipynb>`_
5. Feature extraction via similarity search: application to atom finding and denosing in electon and scanning probe microscopy imaging by S. Somnath et al.; under review at Advanced Structural and Chemical Imaging (2017), jupyter notebook `here 5 <http://nbviewer.jupyter.org/github/pycroscopy/pycroscopy/blob/master/jupyter_notebooks/Image_Cleaning_Atom_Finding.ipynb>`_
5. `Decoding apparent ferroelectricity in perovskite nanofibers <http://pubs.acs.org/doi/pdf/10.1021/acsami.7b14257>`_ by R. Ganeshkumar et al., ACS Applied Materials & Interfaces (2017).
6. Many more coming soon....
6. Ultrafast Current Imaging via Bayesian Inference by S. Somnath et al., accepted at Nature Communications (2017).
7. Feature extraction via similarity search: application to atom finding and denosing in electon and scanning probe microscopy imaging by S. Somnath et al.; under review at Advanced Structural and Chemical Imaging (2017), jupyter notebook `here 5 <http://nbviewer.jupyter.org/github/pycroscopy/pycroscopy/blob/master/jupyter_notebooks/Image_Cleaning_Atom_Finding.ipynb>`_
8. Many more coming soon....
International conferences and workshops using pycroscopy
--------------------------------------------------------
......
......@@ -34,13 +34,20 @@ New features
------------
Core development
~~~~~~~~~~~~~~~~
* Generic interactive visualizer for 3 and 4D float numpy arrays.
* No need to handle h5py datasets, compound datasets, complex datasets etc.
* Add features time permitting.
* Clean up Cluser results plotting
* Consider implementing doSVD as a Process. Maybe the Decomposition and Cluster classes could extend Process?
* Simplify and demystify analyis / optimize. Use parallel_compute instead of optimize and gues_methods and fit_methods
* multi-node computing capability in parallel_compute
* Data Generators
* Consistency in the naming of and placement of attributes (chan or meas group) in all translators
GUI
~~~~~~~~~~~
* Need to be able to run a visualizer even on sliced data. What would this object be? (sliced Main data + vectors for each axis + axis labels ....). Perhaps the slice() function should return this object instead of a numpy array? As it stands, the additional information (for the visualizer) is not returned by the slice function.
* Generic visualizer in plot.lly / dash? that can use the PycroDataset class
* One suggestion is 2 (or more panes).
......
......@@ -122,7 +122,7 @@ dataset would be structured as:
+------------+------------+------------+--------+--------------+--------------+
| i0, j0 | i0, j1 | i0, j2 | .... | i0, jP-2 | i0, jP-1 |
+============+============+============+========+==============+==============+
+------------+------------+------------+--------+--------------+--------------+
| i1, j0 | i1, j1 | i1, j2 | .... | i1, jP-2 | i1, jP-1 |
+------------+------------+------------+--------+--------------+--------------+
| ........ | ........ | ........ | .... | .......... | .......... |
......
......@@ -9,17 +9,25 @@ pycroscopy\.processing\.fft
.. autosummary::
are_compatible_filters
build_composite_freq_filter
downSample
getNoiseFloor
get_fft_stack
harmonicsPassFilter
makeLPF
noiseBandFilter
.. rubric:: Classes
.. autosummary::
FrequencyFilter
HarmonicPassFilter
LowPassFilter
NoiseBandFilter
......
......@@ -9,8 +9,7 @@ pycroscopy\.processing\.giv\_utils
.. autosummary::
bayesian_inference_dataset
bayesian_inference_unit
bayesian_inference_on_period
do_bayesian_inference
plot_bayesian_results
plot_bayesian_spot_from_h5
......
......@@ -10,12 +10,8 @@ pycroscopy\.processing\.gmode\_utils
.. autosummary::
decompress_response
fft_filter_dataset
filter_chunk_parallel
filter_chunk_serial
reshape_from_lines_to_pixels
test_filter
unit_filter
......
......@@ -16,6 +16,7 @@ pycroscopy\.viz\.plot\_utils
export_fig_data
get_cmap_object
make_linear_alpha_cmap
make_scalar_mappable
plotScree
plot_1d_spectrum
plot_2d_spectrogram
......
......@@ -9,9 +9,9 @@ Examples using ``pycroscopy.MicroDataGroup``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_microdata_example_thumb.png
.. figure:: /auto_examples/images/thumb/sphx_glr_plot_microdata_example_thumb.png
:ref:`sphx_glr_auto_examples_microdata_example.py`
:ref:`sphx_glr_auto_examples_plot_microdata_example.py`
.. raw:: html
......@@ -19,7 +19,7 @@ Examples using ``pycroscopy.MicroDataGroup``
.. only:: not html
* :ref:`sphx_glr_auto_examples_microdata_example.py`
* :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
.. raw:: html
......@@ -27,9 +27,9 @@ Examples using ``pycroscopy.MicroDataGroup``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_02_writing_to_h5_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_02_writing_to_h5_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_02_writing_to_h5.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
......@@ -37,7 +37,7 @@ Examples using ``pycroscopy.MicroDataGroup``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_02_writing_to_h5.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
......@@ -45,9 +45,9 @@ Examples using ``pycroscopy.MicroDataGroup``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_05_data_processing_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_05_data_processing.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
......@@ -55,4 +55,40 @@ Examples using ``pycroscopy.MicroDataGroup``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_05_data_processing.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_02_writing_to_h5_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath**">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
......@@ -9,9 +9,9 @@ Examples using ``pycroscopy.MicroDataset``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_microdata_example_thumb.png
.. figure:: /auto_examples/images/thumb/sphx_glr_plot_microdata_example_thumb.png
:ref:`sphx_glr_auto_examples_microdata_example.py`
:ref:`sphx_glr_auto_examples_plot_microdata_example.py`
.. raw:: html
......@@ -19,7 +19,7 @@ Examples using ``pycroscopy.MicroDataset``
.. only:: not html
* :ref:`sphx_glr_auto_examples_microdata_example.py`
* :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
.. raw:: html
......@@ -27,9 +27,9 @@ Examples using ``pycroscopy.MicroDataset``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_02_writing_to_h5_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_02_writing_to_h5_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_02_writing_to_h5.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
......@@ -37,7 +37,7 @@ Examples using ``pycroscopy.MicroDataset``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_02_writing_to_h5.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
......@@ -45,9 +45,9 @@ Examples using ``pycroscopy.MicroDataset``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_05_data_processing_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_05_data_processing.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
......@@ -55,4 +55,40 @@ Examples using ``pycroscopy.MicroDataset``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_05_data_processing.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_02_writing_to_h5_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath**">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
......@@ -9,9 +9,9 @@ Examples using ``pycroscopy.NumpyTranslator``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_01_translator_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_01_translator_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_01_translator.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_translator.py`
.. raw:: html
......@@ -19,4 +19,22 @@ Examples using ``pycroscopy.NumpyTranslator``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_01_translator.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_translator.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_01_translator_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_01_translator.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_01_translator.py`
......@@ -9,9 +9,9 @@ Examples using ``pycroscopy.Process``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_05_data_processing_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_05_data_processing.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
......@@ -19,4 +19,22 @@ Examples using ``pycroscopy.Process``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_05_data_processing.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath**">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
......@@ -9,9 +9,9 @@ Examples using ``pycroscopy.PycroDataset``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_03_multidimensional_data_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_03_multidimensional_data_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_03_multidimensional_data.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
......@@ -19,4 +19,22 @@ Examples using ``pycroscopy.PycroDataset``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_03_multidimensional_data.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_03_multidimensional_data_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_03_multidimensional_data.py`
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