Merge branch 'master' of https://github.com/kushalkolar/MESmerize

kushalkolar · Jul 16, 2020 · 738e24a · 738e24a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,14 @@
+# 0.2.3
+
+### Fixed
+- Batch Manager view input bug with multiple viewers.
+- Transmission.from_proj() bug spiking data are None.
+
+### Modified
+- Transmissions spawned from Load_Proj_DF node no longer have the ``last_output`` attribute set to ``"_RAW_CURVE"``. This allows the ``"_DFOF"`` and ``"_SPIKES"`` data to be used immediately with certain nodes.
+- Units combobox for stimulus mapping module is disabled.
+- Doc links in Help menus now point to the online docs for the current Mesmerize version instead of having built-in docs.
+
 # 0.2.2
 
 ### Fixed

diff --git a/ISSUE_TEMPLATE.md b/ISSUE_TEMPLATE.md
@@ -1,11 +1,9 @@
 ## Operating System
 
 ## Details about your Mesmerize install
-  - **Are you using the snap?**
-  - **which branch if cloned from github?**
-  - **are you using anaconda or venvs (the python built-in virtual environment management)** 
-
-## Mesmerize version (v0.1 or v0.2)
+  - **Are you using the pip install? If so which version?**
+  - **Are you using a clone of the master branch from the GitHub repo?**
+  - **are you using anaconda or venv (the python built-in virtual environment management)** 
 
 ## Describe the issue, please be as explicit and detailed as possible.
 

diff --git a/README.md b/README.md
@@ -15,6 +15,15 @@ Associated bioRxiv paper: https://doi.org/10.1101/840488
 <img src="https://www.biorxiv.org/sites/default/files/site_logo/bioRxiv_logo_homepage.png" alt="manuscript on biorxiv" width="160"/>
 </a>
 
+## Video Tutorials!
+We have recently created detailed video tutorials! The main tutorial series provides a quick overview that takes you from raw imaging data, to downstream analysis and interactive visualizations:\
+https://www.youtube.com/playlist?list=PLgofWiw2s4REPxH8bx8wZo_6ca435OKqg
+
+Additional videos on specific aspects of Mesmerize will be posted here:\
+[https://www.youtube.com/playlist?list=PLgofWiw2s4RF_RkGRUfflcj5k5KUTG3o_](https://www.youtube.com/playlist?list=PLgofWiw2s4RF_RkGRUfflcj5k5KUTG3o_)
+
+More tutorial videos will be available soon.
+
 ## Installation
 
 If you're familiar with anaconda or virtual environments, installation is as simple as:

diff --git a/docs/source/api_reference/Viewer_data_types.rst b/docs/source/api_reference/Viewer_data_types.rst
@@ -3,6 +3,14 @@
 Viewer Core
 ***********
 
+Video Tutorial
+==============
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/a1UO2-OhIHw" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+
 .. _API_ViewerWorkEnv:
 
 ViewerWorkEnv

diff --git a/docs/source/api_reference/viewer_modules/roi_manager.rst b/docs/source/api_reference/viewer_modules/roi_manager.rst
@@ -2,11 +2,19 @@
 
 ROI Manager
 ***********
-The GUI QDockWidget that communicates with the :ref:`back-end managers <API_ROIManagers>`
+
+Video Tutorial
+==============
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/a1UO2-OhIHw" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 
 ModuleGUI
 =========
 
+The GUI QDockWidget that communicates with the :ref:`back-end managers <API_ROIManagers>`
+
 .. autoclass:: mesmerize.viewer.modules.roi_manager.ModuleGUI
     :special-members:
     :members:
@@ -24,6 +32,8 @@ The managers hold instances of :ref:`ROIs <API_ROITYPES>` in an instance of :ref
 AbstractBaseManager
 -------------------
 
+Subclass this if you want to make your own Manager Back-end.
+
 .. autoclass:: mesmerize.viewer.modules.roi_manager_modules.managers.AbstractBaseManager
     :special-members:
     :members:
@@ -106,6 +116,8 @@ AbstractBaseROI
 BaseROI
 -------
 
+Subclass from this if you want to make your own ROI Type.
+
 .. autoclass:: mesmerize.viewer.modules.roi_manager_modules.roi_types.BaseROI
     :show-inheritance:
     :members: __init__, get_roi_graphics_object, set_roi_graphics_object, reset_color, set_original_color, get_color, set_color, set_text, set_tag, get_tag, get_all_tags, add_to_viewer, remove_from_viewer, to_state, from_state

diff --git a/docs/source/banner.png b/docs/source/banner.png
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -3,8 +3,11 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to Mesmerize's documentation!
-=====================================
+Mesmerize Documentation
+***********************
+
+.. image:: ./banner.png
+
 
 | biorxiv: https://doi.org/10.1101/840488
 | GitHub: https://github.com/kushalkolar/MESmerize
@@ -13,7 +16,23 @@ Welcome to Mesmerize's documentation!
 
 .. |gitter_badge| image:: https://badges.gitter.im/mesmerize_discussion/community.svg
                     :target: https://gitter.im/mesmerize_discussion/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge
-
+
+New: Video Tutorials!
+=====================
+
+**The Main Overview Tutorial playlist provides a quick overview that takes you from raw imaging data, to downstream analysis and interactive visualizations:**
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?list=PLgofWiw2s4REPxH8bx8wZo_6ca435OKqg" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+|
+
+**Additional tutorials on other aspects of Mesmerize will be placed in this playlist:**
+https://www.youtube.com/playlist?list=PLgofWiw2s4RF_RkGRUfflcj5k5KUTG3o_
+
+
+
 .. toctree::
 	:maxdepth: 1
 	:caption: Overview

diff --git a/docs/source/user_guides/flowchart/examples.rst b/docs/source/user_guides/flowchart/examples.rst
@@ -3,6 +3,9 @@
 Examples
 ********
 
+Datasets
+========
+
 You can view examples of flowcharts in the demo dataset or one of the other datasets associated with the paper:
 
 Demo dataset: https://doi.org/10.6084/m9.figshare.11370183
@@ -13,6 +16,35 @@ C. elegans dataset: https://doi.org/10.6084/m9.figshare.10287113
 
 PVC-7 as a Mesmerize dataset: https://doi.org/10.6084/m9.figshare.10293041
 
+
+Video Tutorials
+===============
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/ghB38QR1yuE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/FtMPmXldf9E" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/mIrps8rJEQ4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/5ucFw3OwCC4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/Z4dNOK0GGBU" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/7Hf1BXzkfFc" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+
 Screenshots
 ===========
 

diff --git a/docs/source/user_guides/flowchart/overview.rst b/docs/source/user_guides/flowchart/overview.rst
@@ -30,6 +30,18 @@ Click on a node to highlight the Control Widget
 
 **Reset View button**: Reset the view, for example if you zoom out or pan too far.
 
+
+Video Tutorial
+==============
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/ghB38QR1yuE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+Part 5 - 9 of the Main Tutorial series also provide various examples for how the flowchart can be used:
+https://www.youtube.com/playlist?list=PLgofWiw2s4REPxH8bx8wZo_6ca435OKqg
+
+
 .. _concept_Transmission:
 
 Transmission

diff --git a/docs/source/user_guides/plots/datapoint_tracer.rst b/docs/source/user_guides/plots/datapoint_tracer.rst
@@ -9,7 +9,20 @@ The Datapoint Tracer is attached to many plots, allowing you to interactively ex
 
 The Datapoint Tracer is embedded in some plots, and in others you can open it by going to View -> Live Datapoint Tracer.
 
-**Datapoint Tracer Layout**
+Video Tutorial
+==============
+
+This tutorial shows how the Heatmap plot can be used along with the Datapoint Tracer during the latter half of this tutorial.
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/ghB38QR1yuE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+Part 5, 6 & 8 of the main tutorial series also show how the Datapoint Tracer can be used along with other types of plots:
+https://www.youtube.com/playlist?list=PLgofWiw2s4REPxH8bx8wZo_6ca435OKqg
+
+Layout
+======
 
 .. image:: ./datapoint_tracer.png
 

diff --git a/docs/source/user_guides/plots/heatmap.rst b/docs/source/user_guides/plots/heatmap.rst
@@ -10,7 +10,17 @@ Heatmap
 
 Visualize numerical arrays in the form of a heatmap. Also used for visualization of Hierarchical clusterting dendrograms. :ref:`DatapointTracer` is embedded.
 
-**Layout**
+Video Tutorial
+==============
+
+This tutorial shows how the Heatmap plot can be used along with the Datapoint Tracer during the latter half of this tutorial.
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/ghB38QR1yuE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+Layout
+======
 
 .. image:: ./heatmap_layout.png
 

diff --git a/docs/source/user_guides/plots/kshape.rst b/docs/source/user_guides/plots/kshape.rst
@@ -194,7 +194,7 @@ Hide legend
 
 Hide/show legend in the proportions plot
 
-.. code-block:: pyton
+.. code-block:: python
 
     get_plot_proportions().ax.legend().set_visible(True)
     get_plot_proportions().draw()

diff --git a/docs/source/user_guides/plots/peak_editor.rst b/docs/source/user_guides/plots/peak_editor.rst
@@ -5,6 +5,17 @@ Peak Editor
 
 Visualize and edit detected peaks & bases. This GUI is accessible through the :ref:`PeakDetect node <node_PeakDetect>`.
 
+Video Tutorial
+==============
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/5ucFw3OwCC4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/Z4dNOK0GGBU" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
 Usage
 =====
 

diff --git a/docs/source/user_guides/plots/scatter.rst b/docs/source/user_guides/plots/scatter.rst
@@ -10,6 +10,14 @@ Scatter
 .. note::
     :ref:`This plot can be saved in an interactive form <save_ptrn>`
 
+Video Tutorial
+==============
+
+From 13:04 onward this tutorial shows how you can perform PCA and visualize the transformed data using the Scatter Plot.
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/FtMPmXldf9E" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 
 Layout
 ======

diff --git a/docs/source/user_guides/plots/spacemap.rst b/docs/source/user_guides/plots/spacemap.rst
@@ -17,6 +17,16 @@ Spatially map a categorical variable onto a projection of a Sample's image seque
     http://dx.doi.org/10.6080/K0C8276G
 
 
+Video Tutorial
+==============
+
+This shows how you can view a space map that shows the tuning of cells. The Space map plot itself is shows after 3:38.
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/FtMPmXldf9E" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+
 Controls
 ========
 

diff --git a/docs/source/user_guides/project_organization/new_project/new_project.rst b/docs/source/user_guides/project_organization/new_project/new_project.rst
@@ -3,6 +3,15 @@
 Create a New Project
 ********************
 
+Video Tutorial
+==============
+
+This tutorial shows how to create a New Project, open images in the Viewer, use the Stimulus Mapping module and perform Caiman motion correction
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/D9zKhFkcKTk" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
 Biological Questions
 ====================
 **Before you create a new Mesmerize Project you must thoroughly think about the biological questions that you are interested in. Here are some thoughts to help you:**

diff --git a/docs/source/user_guides/viewer/add_to_project.rst b/docs/source/user_guides/viewer/add_to_project.rst
@@ -31,3 +31,10 @@ Every Sample in a project has a unique **SampleID** which is the combination of
 .. warning:: AnimalID and TrialID are separated by the ``-_-`` character combination when stored as a SampleID. Therefore do not use that character combination within your AnimalID or TrialID.
 
 
+Video Tutorial
+==============
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/0iWV7NRock4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
diff --git a/docs/source/user_guides/viewer/modules/batch_manager.rst b/docs/source/user_guides/viewer/modules/batch_manager.rst
@@ -7,6 +7,15 @@ Batch Manager
 
 .. seealso:: :ref:`Batch Manager API <API_BatchManager>`
 
+Video Tutorial
+==============
+
+This tutorial shows how to create a New Project, open images in the Viewer, use the Stimulus Mapping module and perform Caiman motion correction
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/D9zKhFkcKTk" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
 This is currently used for :ref:`Caiman Motion Correction <module_CaimanMotionCorrection>`, :ref:`CNMF <module_CNMF>`, :ref:`CNMF 3D <module_CNMF_3D>` and  :ref:`CNMFE <module_CNMFE>`.
 
 The Batch Manager can be accessed in the viewer through Modules -> Batch Manager. If you don't have a batch open you will be prompted with a dialog to open a batch or to select a location for a new batch.

diff --git a/docs/source/user_guides/viewer/modules/roi_manager.rst b/docs/source/user_guides/viewer/modules/roi_manager.rst
@@ -18,6 +18,15 @@ The ROI Manager has a manual mode, to draw ROIs manually, and a CNMF(E) mode whe
 
 The ImageJ ROI import uses the read-roi package by Hadrien Mary https://pypi.org/project/read-roi/
 
+
+Video Tutorial
+==============
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/0iWV7NRock4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+
 Layout
 ======
 

diff --git a/docs/source/user_guides/viewer/modules/stimulus_mapping.rst b/docs/source/user_guides/viewer/modules/stimulus_mapping.rst
@@ -5,6 +5,16 @@ Stimulus Mapping
 
 :ref:`API Reference <API_StimulusMapping>`
 
+Video Tutorial
+==============
+
+This tutorial shows how to create a New Project, open images in the Viewer, use the Stimulus Mapping module and perform Caiman motion correction
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/D9zKhFkcKTk" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+
 **Map temporal information such as stimulus or behavioral periods.**
 
 Stimulus Mapping Module

diff --git a/docs/source/user_guides/viewer/modules/suite2p_importer.rst b/docs/source/user_guides/viewer/modules/suite2p_importer.rst
@@ -7,6 +7,16 @@ You can load Suite2p output files to import ROIs into the current :ref:`work env
 
 .. image:: ./suite2p_importer.png
 
+Video Tutorial
+==============
+
+.. raw:: html
+
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/OvGfrdRSNE8" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+Script Usage
+============
+
 You can also use this module through the :ref:`viewer console <ViewerConsole>`, or in the :ref:`Script Editor <module_ScriptEditor>` instead of clicking buttons.
 
 **Example**