From 14663a75b8ed7d3b09952447d0c4dff9fa7ebe04 Mon Sep 17 00:00:00 2001
From: Antognetti <broantognetti@gmail.com>
Date: Mon, 20 May 2024 11:28:45 -0500
Subject: [PATCH 01/12] Draft for beginning to implement xarray as containers
 for data from MDSPlus

---
 src/wipplpy/modules/generic_get_data.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index 1eb1f49..eec0eda 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -521,6 +521,8 @@ def get(  # noqa: PLR0912, PLR0915
                     )
                     try_loading = True
                     self.tree = get_remote_shot_tree(self.shot_number, reconnect=True)
+        
+        #Going to be changing to put into xarray arrays
 
         if self.ignore_errors:
             try:
@@ -535,7 +537,7 @@ def get(  # noqa: PLR0912, PLR0915
             data = data.astype(np_data_type)
             logging.debug(f"Changed data to type '{np_data_type}'.")
 
-        # Only save calls if the dictionary exists. The dictionary doesn't exist during some stages of initialization so that we don't save incorrect data.
+        # Only save calls if the dictionary exists. Th dictionary doesn't exist during some stages of initialization so that we don't save incorrect data.
         if hasattr(self, "saved_calls"):
             # logging.debug("Adding data from get call with `save_name='{}'` into `saved_calls`.".format(save_name))
             if save_name in self.saved_calls:
@@ -543,7 +545,7 @@ def get(  # noqa: PLR0912, PLR0915
                     "Save name ({}) is the same as a save name already in the data to save dictionary. Overwriting old data."
                 )
             self.saved_calls[save_name] = data
-
+        #
         return data
 
     def to_raw_index(self, time_index):

From 859259d08f6a5953c8b3a11febe8b05649c80f7e Mon Sep 17 00:00:00 2001
From: Antognetti <broantognetti@gmail.com>
Date: Mon, 20 May 2024 12:01:03 -0500
Subject: [PATCH 02/12] Added xarray to environment dependencies

---
 mamba_environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mamba_environment.yml b/mamba_environment.yml
index 62df5eb..b596316 100644
--- a/mamba_environment.yml
+++ b/mamba_environment.yml
@@ -14,3 +14,4 @@ dependencies:
   - configobj
   - pyyaml
   - sphinx
+  - xarray
\ No newline at end of file

From b1f7b5bf6b5381727517d19ba5999a0392e8449a Mon Sep 17 00:00:00 2001
From: Antognetti <broantognetti@gmail.com>
Date: Thu, 23 May 2024 13:05:37 -0500
Subject: [PATCH 03/12] Introduced gather_DataArray and package_DataSet
 function

---
 src/wipplpy/modules/generic_get_data.py | 34 ++++++++++++++++++++++---
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index eec0eda..140e4f7 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -2,6 +2,7 @@
 import re
 
 import numpy as np
+import xarray as xr
 from MDSplus.connection import Connection, MdsIpException
 from MDSplus.mdsExceptions import MDSplusException, SsSUCCESS
 from wipplpy.modules.shot_loader import get_remote_shot_tree 
@@ -429,7 +430,7 @@ def _get_many(self, tree, variable_booleans, get_calls):
         return variable_vals
 
     def get(  # noqa: PLR0912, PLR0915
-        self, get_call, np_data_type=np.float64, change_data=True, load_from_saved=True
+        self, get_call, np_data_type=np.float64, change_data=True, load_from_saved=True,
     ):
         """
         Get data from the mdsplus tree and change it to the correct type using a get call.
@@ -521,8 +522,6 @@ def get(  # noqa: PLR0912, PLR0915
                     )
                     try_loading = True
                     self.tree = get_remote_shot_tree(self.shot_number, reconnect=True)
-        
-        #Going to be changing to put into xarray arrays
 
         if self.ignore_errors:
             try:
@@ -545,8 +544,35 @@ def get(  # noqa: PLR0912, PLR0915
                     "Save name ({}) is the same as a save name already in the data to save dictionary. Overwriting old data."
                 )
             self.saved_calls[save_name] = data
+
+        self.to_xarray(data, xarray_args=xarray_args, xarray_kwargs=xarray_kwargs)
+    
+    def gather_to_xarray(self, path):
+        """
+        Package data along with dimensions and attributes into an xarray DataArray. Pulls data from MDSPlus or local files.
+        """
+        #get data first as numpy array
+        #get dimensions of array
+        #   spatial ()
+        #   time (add sampling rate as attribute, might be unnecessary)
+        #get coordinates for dimensions that need it
+        #units on dimensions (is this stored as an attribute of the array or of the coord)
+        #fill in attributes (e.g. machine, maybe port info)
+        #
+        #data = get(path)
         #
-        return data
+        #data_array = xr.DataArray(data)
+        #any other additions to the DataArray
+        #self.data = data_array
+        pass
+
+    def package_as_DataSet(self, path_list):
+        '''
+        Gather and combine multiple xarray DataArrays into a single DataSet. May
+        have multiple calls to gather_to_xarray, or maybe can also pass in DataArrays
+        explicitly which have already been put together.
+        '''
+        pass
 
     def to_raw_index(self, time_index):
         """

From 3719363508946d966cd8cabc02064d4a52ca5976 Mon Sep 17 00:00:00 2001
From: Antognetti <broantognetti@gmail.com>
Date: Thu, 13 Jun 2024 15:30:53 -0500
Subject: [PATCH 04/12] Building coordinate dictionary

---
 src/wipplpy/modules/generic_get_data.py | 39 +++++++++++++++++--------
 1 file changed, 27 insertions(+), 12 deletions(-)

diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index 140e4f7..3845663 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -545,31 +545,46 @@ def get(  # noqa: PLR0912, PLR0915
                 )
             self.saved_calls[save_name] = data
 
-        self.to_xarray(data, xarray_args=xarray_args, xarray_kwargs=xarray_kwargs)
+        return data
     
-    def gather_to_xarray(self, path):
+    def gather_DataArray(self, node, dim_names):
         """
         Package data along with dimensions and attributes into an xarray DataArray. Pulls data from MDSPlus or local files.
+        
+        Parameters
+        ----------
+        node : str
+            MDSPlus node for the wanted data. 
+
+        Returns
+        -------
+        array : xr.DataArray
+            DataArray with stored data and metadata
+        
         """
         #get data first as numpy array
-        #get dimensions of array
-        #   spatial ()
-        #   time (add sampling rate as attribute, might be unnecessary)
+        data = node.data()
+        ndim = data.ndim 
+        if ndim != len(dim_names): raise Exception("Number of dimension names and dimenion of data do not match")
+
+        coords = {}
+        #dim_units = {}
+        for dim in range(ndim):
+            coords[dim_names[dim]] = data.dim_of(dim).data()
+            
         #get coordinates for dimensions that need it
         #units on dimensions (is this stored as an attribute of the array or of the coord)
-        #fill in attributes (e.g. machine, maybe port info)
-        #
-        #data = get(path)
-        #
+        #fill in attributes 
+        #maybe summary info like average Ip, ne, Bt, q (what would be some equivalent things for BRB? ) but what would be the resource cost for this?
+        #maybe main contact person + their email for the diagnostic
         #data_array = xr.DataArray(data)
-        #any other additions to the DataArray
         #self.data = data_array
         pass
 
-    def package_as_DataSet(self, path_list):
+    def package_DataSet(self, path_list):
         '''
         Gather and combine multiple xarray DataArrays into a single DataSet. May
-        have multiple calls to gather_to_xarray, or maybe can also pass in DataArrays
+        have multiple calls to gather_to_DataArray. Could also be passed DataArrays
         explicitly which have already been put together.
         '''
         pass

From 6f9f40c1d59e55de9e1df9d683919e95f67f4929 Mon Sep 17 00:00:00 2001
From: Antognetti <broantognetti@gmail.com>
Date: Thu, 13 Jun 2024 16:06:28 -0500
Subject: [PATCH 05/12] First xarray DataArray

---
 src/wipplpy/modules/generic_get_data.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index 3845663..bff1ed2 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -577,8 +577,9 @@ def gather_DataArray(self, node, dim_names):
         #fill in attributes 
         #maybe summary info like average Ip, ne, Bt, q (what would be some equivalent things for BRB? ) but what would be the resource cost for this?
         #maybe main contact person + their email for the diagnostic
-        #data_array = xr.DataArray(data)
-        #self.data = data_array
+
+        data_array = xr.DataArray(data, dims = dim_names, coords = coords)
+        self.data = data_array
         pass
 
     def package_DataSet(self, path_list):

From 9b4fad8c43dafba1f9b24e82e31b5915a8218b59 Mon Sep 17 00:00:00 2001
From: Antognetti <broantognetti@gmail.com>
Date: Fri, 6 Sep 2024 09:48:34 -0500
Subject: [PATCH 06/12] renamed gather_DataArray to gather_data_array

---
 docs/source/contributing.rst            |  4 +-
 docs/source/installation.rst            | 63 +++++++++++------------
 src/wipplpy/modules/generic_get_data.py | 67 +++++++++++++------------
 3 files changed, 70 insertions(+), 64 deletions(-)

diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
index d945d53..94d999a 100644
--- a/docs/source/contributing.rst
+++ b/docs/source/contributing.rst
@@ -4,6 +4,6 @@
 Contributing
 ************
 
-We follow the same design as PlasmaPy for contributing. Please see the `PlasmaPy 
-contributing workflow guide <https://docs.plasmapy.org/en/stable/contributing/workflow.html>`_ 
+We follow the same design as PlasmaPy for contributing. Please see the `PlasmaPy
+contributing workflow guide <https://docs.plasmapy.org/en/stable/contributing/workflow.html>`_
 for more information.
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index 4867e7d..9ca2b50 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -7,7 +7,7 @@ Installation
 Installing WiPPLPy as a Contributor
 ===================================
 
-This installation is very similar to how PlasmaPy installation is done for 
+This installation is very similar to how PlasmaPy installation is done for
 contributors: https://docs.plasmapy.org/en/stable/contributing/getting_ready.html.
 We've done some copy-pasting as to which steps should be followed.
 
@@ -19,8 +19,8 @@ Pre-requisites
 Opening a terminal
 ^^^^^^^^^^^^^^^^^^
 
-The commands in this page are intended to be run in a ``Unix`` terminal. If you 
-are new to Unix, check out this `Unix tutorial`_ and these `frequently used 
+The commands in this page are intended to be run in a ``Unix`` terminal. If you
+are new to Unix, check out this `Unix tutorial`_ and these `frequently used
 Unix commands`_.
 
 Windows
@@ -28,19 +28,19 @@ Windows
 
 There are several options for terminals on Windows.
 
-* Powershell_ comes pre-installed with Windows. These instructions cover 
-  `opening Powershell`_. We recommend Powershell for a quick start, if Windows 
+* Powershell_ comes pre-installed with Windows. These instructions cover
+  `opening Powershell`_. We recommend Powershell for a quick start, if Windows
   is the only operating system you use, or if you have not used Unix before.
 
-* We recommend `Windows Subsystem for Linux`_ (WSL) if you are familiar with 
-  Unix, you use macOS or Linux too, or you expect to contribute to WiPPLPy 
-  extensively. These instructions cover `installing WSL`_. If you choose WSL, 
+* We recommend `Windows Subsystem for Linux`_ (WSL) if you are familiar with
+  Unix, you use macOS or Linux too, or you expect to contribute to WiPPLPy
+  extensively. These instructions cover `installing WSL`_. If you choose WSL,
   follow the tabs for :guilabel:`Linux/WSL` below.
 
 macOS
 """""
 
-In the :guilabel:`Finder`, go to :guilabel:`Applications`. Enter the 
+In the :guilabel:`Finder`, go to :guilabel:`Applications`. Enter the
 :guilabel:`Utilities` folder and double click on :guilabel:`Terminal`.
 
 Linux/WSL
@@ -53,12 +53,12 @@ Open a terminal by using :kbd:`Ctrl + Alt + T`.
 Installing Python
 ^^^^^^^^^^^^^^^^^
 
-We suggest using Mamba_ to install Python_. Mamba_ is a versatile package and 
-environment management system which is widely used in the data science and 
-scientific Python communities that is similar to Conda_. It is a command line 
-interface for installing packages. 
+We suggest using Mamba_ to install Python_. Mamba_ is a versatile package and
+environment management system which is widely used in the data science and
+scientific Python communities that is similar to Conda_. It is a command line
+interface for installing packages.
 
-* If you already have Conda_ installed, then follow the `installing Mamba from 
+* If you already have Conda_ installed, then follow the `installing Mamba from
   an existing Conda install`_.
 
 * Otherwise, follow the `installing Mamba`_ instructions.
@@ -109,7 +109,7 @@ contributing code to WiPPLPy, please take the following steps:
 Installing Your Clone of WiPPLPy
 --------------------------------
 
-Once Mamba_ is installed and you have cloned the git repository then we need to 
+Once Mamba_ is installed and you have cloned the git repository then we need to
 create an environment for running the code in.
 
 1. :ref:`Open a terminal <opening-a-terminal>`.
@@ -126,8 +126,8 @@ create an environment for running the code in.
 
       In Windows, the directory path will be :file:`C:\\Users\\<username>\\repos\\WiPPLPy`.
 
-3. Create a Mamba_ environment using the packages from 
-   :file:`mamba_environment.yml`. If you are on a computer that does not use 
+3. Create a Mamba_ environment using the packages from
+   :file:`mamba_environment.yml`. If you are on a computer that does not use
    the Mac silicon processor you can do so by running
 
    .. code-block:: bash
@@ -149,30 +149,32 @@ create an environment for running the code in.
       mamba activate WiPPLPy
       python
 
-5. We need to add the :file:`WiPPLPy/source/` directory to the Python path. We 
-   can find the path to :file:`WiPPLPy/source/` and the :file:`site-packages` 
+5. We need to add the :file:`WiPPLPy/source/` directory to the Python path. We
+   can find the path to :file:`WiPPLPy/source/` and the :file:`site-packages`
    directory by running the following Python code:
 
    .. code-block:: python
 
       from distutils.sysconfig import get_python_lib
-      print('site-packaged directory:', get_python_lib())
+
+      print("site-packaged directory:", get_python_lib())
       import os
-      print('WiPPLPy source code directory:', os.getcwd())
 
-6. Exit out of python and navigate to the :file:`site-packages` directory that 
+      print("WiPPLPy source code directory:", os.getcwd())
+
+6. Exit out of python and navigate to the :file:`site-packages` directory that
    was printed. It should end in :file:`site-packages`.
 
-7. Create a file called :file:`wipplpy.pth`. This file should contain the path 
-   to the :file:`WiPPLPy/src/` directory. For example, if the path to the 
-   :file:`WiPPLPy/src/` directory is :file:`/Users/username/repos/WiPPLPy/src/` 
+7. Create a file called :file:`wipplpy.pth`. This file should contain the path
+   to the :file:`WiPPLPy/src/` directory. For example, if the path to the
+   :file:`WiPPLPy/src/` directory is :file:`/Users/username/repos/WiPPLPy/src/`
    then the :file:`wipplpy.pth` file should contain the following:
 
    .. code-block:: bash
 
       /Users/username/repos/WiPPLPy/src/
 
-8. Test that the installation was successful by running the following Python 
+8. Test that the installation was successful by running the following Python
    code:
 
    .. code-block:: python
@@ -185,16 +187,16 @@ create an environment for running the code in.
 Creating Documentation
 ======================
 
-To create the documentation, you will need to have `Sphinx`_ installed and 
+To create the documentation, you will need to have `Sphinx`_ installed and
 `make`_. This should have already been installed when you created your Mamba environment.
 
-Then, you can create the documentation by entering the ``docs/`` directory and 
+Then, you can create the documentation by entering the ``docs/`` directory and
 running the following command::
 
     make html
 
-This will create the documentation in the :file:`docs/build/html/` directory. 
-Open the documentation by double clicking on the :file:`index.html` file in the 
+This will create the documentation in the :file:`docs/build/html/` directory.
+Open the documentation by double clicking on the :file:`index.html` file in the
 :file:`docs/build/html/` directory.
 
 .. _Sphinx: https://www.sphinx-doc.org/en/master/usage/installation.html
@@ -233,4 +235,3 @@ Open the documentation by double clicking on the :file:`index.html` file in the
 .. _WSL: https://learn.microsoft.com/en-us/windows/wsl
 .. _git: https://git-scm.com
 .. _GitHub: https://github.com
-
diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index bff1ed2..126f9a7 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -5,9 +5,10 @@
 import xarray as xr
 from MDSplus.connection import Connection, MdsIpException
 from MDSplus.mdsExceptions import MDSplusException, SsSUCCESS
-from wipplpy.modules.shot_loader import get_remote_shot_tree 
 from scipy.io import loadmat, savemat
 
+from wipplpy.modules.shot_loader import get_remote_shot_tree
+
 
 # This lazy get property is taken from https://towardsdatascience.com/what-is-lazy-evaluation-in-python-9efb1d3bfed0
 def lazy_get(function):
@@ -430,7 +431,11 @@ def _get_many(self, tree, variable_booleans, get_calls):
         return variable_vals
 
     def get(  # noqa: PLR0912, PLR0915
-        self, get_call, np_data_type=np.float64, change_data=True, load_from_saved=True,
+        self,
+        get_call,
+        np_data_type=np.float64,
+        change_data=True,
+        load_from_saved=True,
     ):
         """
         Get data from the mdsplus tree and change it to the correct type using a get call.
@@ -546,49 +551,49 @@ def get(  # noqa: PLR0912, PLR0915
             self.saved_calls[save_name] = data
 
         return data
-    
-    def gather_DataArray(self, node, dim_names):
+
+    def gather_data_array(self, node, dimension_names, dimension_units):
         """
         Package data along with dimensions and attributes into an xarray DataArray. Pulls data from MDSPlus or local files.
-        
+
         Parameters
         ----------
         node : str
-            MDSPlus node for the wanted data. 
+            MDSPlus node for the chosen data.
+        dimension_names : list[str]
+            list of human readable dimension names. Should be consistent with WiPPLPy conventions --insert a link here to some info about common WiPPLPy dimensions and conventions
+        dimension_units : list[str]
+            List of dimension units. Should be in a format consistent with astropy.units https://docs.astropy.org/en/stable/units/
 
         Returns
         -------
         array : xr.DataArray
             DataArray with stored data and metadata
-        
+
         """
-        #get data first as numpy array
+        # get data first as numpy array
         data = node.data()
-        ndim = data.ndim 
-        if ndim != len(dim_names): raise Exception("Number of dimension names and dimenion of data do not match")
+        num_dimensions = data.ndim
+        if num_dimensions != len(dimension_names):
+            raise Exception(
+                "Number of dimension names and number of data dimensions do not match"
+            )
 
         coords = {}
-        #dim_units = {}
-        for dim in range(ndim):
-            coords[dim_names[dim]] = data.dim_of(dim).data()
-            
-        #get coordinates for dimensions that need it
-        #units on dimensions (is this stored as an attribute of the array or of the coord)
-        #fill in attributes 
-        #maybe summary info like average Ip, ne, Bt, q (what would be some equivalent things for BRB? ) but what would be the resource cost for this?
-        #maybe main contact person + their email for the diagnostic
-
-        data_array = xr.DataArray(data, dims = dim_names, coords = coords)
-        self.data = data_array
-        pass
-
-    def package_DataSet(self, path_list):
-        '''
-        Gather and combine multiple xarray DataArrays into a single DataSet. May
-        have multiple calls to gather_to_DataArray. Could also be passed DataArrays
-        explicitly which have already been put together.
-        '''
-        pass
+        dimension_units = {}
+
+        for dim_num, dim_name in dimension_names:
+            coords[dim_name] = data.dim_of(dim_num).data()
+            dimension_units[dim_name] = dimension_units
+
+        # get coordinates arrays for dimensions that need it
+
+        # get the rest of the attributes together into
+        {"units": dimension_units}
+
+        data_array = xr.DataArray(data, dims=dimension_names, coords=coords)
+
+        return data_array
 
     def to_raw_index(self, time_index):
         """

From 25df186b54efca935c56a4242db3cd3fb75cafab Mon Sep 17 00:00:00 2001
From: Antognetti <broantognetti@gmail.com>
Date: Thu, 7 Nov 2024 18:48:05 -0600
Subject: [PATCH 07/12] Changed get to call gather_data_array directly

---
 src/wipplpy/modules/generic_get_data.py | 43 +++++++++++++++----------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index bdb665b..152ddda 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -406,11 +406,7 @@ def _get_many(self, tree, variable_booleans, get_calls):
         return variable_vals
 
     def get(  # noqa: PLR0912, PLR0915
-        self,
-        get_call,
-        np_data_type=np.float64,
-        change_data=True,
-        load_from_saved=True,
+        self, get_call, np_data_type=np.float64, change_data=True, load_from_saved=True
     ):
         """
         Get data from the mdsplus tree and change it to the correct type using a get call.
@@ -425,6 +421,8 @@ def get(  # noqa: PLR0912, PLR0915
             Whether to change the data type of what MDSplus returns.
         load_from_saved : bool, default=True
             Whether to try to load the data from the saved calls.
+        return_node : bool, default = False
+            Whether to return the data node instead of returning the data itself. Used for gathering xarray.
 
         Returns
         -------
@@ -493,20 +491,21 @@ def get(  # noqa: PLR0912, PLR0915
                     try_loading = True
                     self.tree = get_remote_shot_tree(self.shot_number, reconnect=True)
 
+        # Might be good to put the rest of these checks into a separate function, so it can be called here and in the gather_data_array
         if self.ignore_errors:
             try:
-                data = node.data()
+                data = self.gather_data_array(node)
             except Exception:
                 return np.array()
         else:
-            data = node.data()
+            data = self.gather_data_array(node)
 
         logging.debug("Got data from tree.")
         if change_data:
             data = data.astype(np_data_type)
             logging.debug(f"Changed data to type '{np_data_type}'.")
 
-        # Only save calls if the dictionary exists. Th dictionary doesn't exist during some stages of initialization so that we don't save incorrect data.
+        # Only save calls if the dictionary exists. The dictionary doesn't exist during some stages of initialization so that we don't save incorrect data.
         if hasattr(self, "saved_calls"):
             # logging.debug("Adding data from get call with `save_name='{}'` into `saved_calls`.".format(save_name))
             if save_name in self.saved_calls:
@@ -517,14 +516,14 @@ def get(  # noqa: PLR0912, PLR0915
 
         return data
 
-    def gather_data_array(self, node, dimension_names, dimension_units):
+    def gather_data_array(self, mds_node, dimension_names=None, dimension_units=None):
         """
         Package data along with dimensions and attributes into an xarray DataArray. Pulls data from MDSPlus or local files.
 
         Parameters
         ----------
-        node : str
-            MDSPlus node for the chosen data.
+        mds_node : MDSPlus.node
+            mdsplus node to which desired data is attached
         dimension_names : list[str]
             list of human readable dimension names. Should be consistent with WiPPLPy conventions --insert a link here to some info about common WiPPLPy dimensions and conventions
         dimension_units : list[str]
@@ -537,11 +536,18 @@ def gather_data_array(self, node, dimension_names, dimension_units):
 
         """
         # get data first as numpy array
-        data = node.data()
+
+        data = mds_node.data()
         num_dimensions = data.ndim
+
+        if len(num_dimensions) != len(dimension_units):
+            raise Exception(
+                "*** Number of dimension names and number of dimension units does not match"
+            )
+
         if num_dimensions != len(dimension_names):
             raise Exception(
-                "Number of dimension names and number of data dimensions do not match"
+                "*** Number of dimension names and number of data dimensions does not match"
             )
 
         coords = {}
@@ -551,14 +557,17 @@ def gather_data_array(self, node, dimension_names, dimension_units):
             coords[dim_name] = data.dim_of(dim_num).data()
             dimension_units[dim_name] = dimension_units
 
-        # get coordinates arrays for dimensions that need it
+        coords["shot_num"] = mds_node.shot
 
         # get the rest of the attributes together into
-        {"units": dimension_units}
+        attributes = {"units": dimension_units, "call_string": "thing", "version": 1.0}
 
-        data_array = xr.DataArray(data, dims=dimension_names, coords=coords)
+        data_xarray = xr.DataArray(
+            data, dims=dimension_names, coords=coords, attrs=attributes
+        )
 
-        return data_array
+        self.xarray = data_xarray  # hmm which one
+        return data_xarray
 
     def to_raw_index(self, time_index):
         """

From 5793022ed314cacb36600afc5042acef442bbc2a Mon Sep 17 00:00:00 2001
From: Antognetti <broantognetti@gmail.com>
Date: Tue, 18 Feb 2025 16:26:13 -0600
Subject: [PATCH 08/12] Removed bug with calling for length of int (silly silly
 me)

---
 src/wipplpy/modules/generic_get_data.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index 152ddda..14c16b4 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -311,6 +311,7 @@ def _to_time_index(self, time):
         index : int
             Data index from start of digitizer recording.
         """
+
         try:
             times = self.time
         except AttributeError:
@@ -540,7 +541,7 @@ def gather_data_array(self, mds_node, dimension_names=None, dimension_units=None
         data = mds_node.data()
         num_dimensions = data.ndim
 
-        if len(num_dimensions) != len(dimension_units):
+        if num_dimensions != len(dimension_units):
             raise Exception(
                 "*** Number of dimension names and number of dimension units does not match"
             )

From 4dd94d24a48fe8d3feaf7b889ab5ef472fc7da21 Mon Sep 17 00:00:00 2001
From: Ben Antognetti <antognetti@wisc.edu>
Date: Tue, 25 Mar 2025 14:45:39 -0500
Subject: [PATCH 09/12] Intermediate commit for moving repo around on MST
 server

---
 mamba_environment_linux.yml                  | 15 ---------------
 src/wipplpy/modules/generic_get_data.py      |  4 +++-
 src/wipplpy/modules/shot_loading_config.json |  4 ++--
 3 files changed, 5 insertions(+), 18 deletions(-)
 delete mode 100644 mamba_environment_linux.yml

diff --git a/mamba_environment_linux.yml b/mamba_environment_linux.yml
deleted file mode 100644
index 90ff2a2..0000000
--- a/mamba_environment_linux.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-name: WiPPLPy
-channels:
-  - defaults
-  - anaconda
-  - conda-forge
-dependencies:
-  - python=3.9
-  - jupyter
-  - numpy
-  - scipy
-  - matplotlib
-  - tqdm
-  - configobj
-  - pyyaml
-  - sphinx
diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index 152ddda..3bea780 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -206,7 +206,9 @@ def __init__(  # noqa: PLR0913
         try:
             self.shot_number = int(tree)
         except ValueError:
-            self.shot_number = tree.shot_number
+            self.shot_number = tree.shot
+        except TypeError:
+            self.shot_number = tree.shot
 
         self.ignore_errors = ignore_errors
         self.silence_error_logging = silence_error_logging
diff --git a/src/wipplpy/modules/shot_loading_config.json b/src/wipplpy/modules/shot_loading_config.json
index 0afc389..50a53f0 100644
--- a/src/wipplpy/modules/shot_loading_config.json
+++ b/src/wipplpy/modules/shot_loading_config.json
@@ -1,4 +1,4 @@
 {
-    "tree_name": "wipal",
-    "server_name": "skywalker.physics.wisc.edu"
+    "tree_name": "mst",
+    "server_name": "toni.physics.wisc.edu"
 }

From 2a41f4b4a128ef7f8b37681501ecc011766e87c5 Mon Sep 17 00:00:00 2001
From: Ben Antognetti <antognetti@wisc.edu>
Date: Tue, 27 May 2025 12:50:17 -0500
Subject: [PATCH 10/12] Returned get to old way

---
 src/wipplpy/modules/generic_get_data.py | 72 ++++++++++++++++---------
 1 file changed, 46 insertions(+), 26 deletions(-)

diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index 456564a..37eccb0 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -68,11 +68,13 @@ def __init__(self, call_string, name=None, signal=True):
             self.name = name
         self.signal = signal
 
+
     def __str__(self) -> str:
         if self.signal:
             return f"Get({self.call_string}, is_signal)"
         else:
             return f"Get({self.call_string})"
+        
 
     def full_str(self, index_range=None, sample_period=1):
         """
@@ -331,6 +333,20 @@ def _to_time_index(self, time):
 
         return index
 
+    def set_array_dimensions(self):
+        """
+        Function to be overwrriten when Data class is implemented for a specific data set
+
+        Parameters
+        ----------
+        dimension_names : list[str]
+            list of human readable dimension names. Should be consistent with WiPPLPy conventions --insert a link here to some info about common WiPPLPy dimensions and conventions--
+        dimension_units : list[str]
+            List of dimension units. Should be in a format consistent with astropy.units https://docs.astropy.org/en/stable/units/
+        """
+        self.dimension_units=[]
+        self.dimension_names=[]
+
     def _get_individuals(self, variable_booleans, get_calls):
         """
         Get all data that has a True boolean associated with it.
@@ -497,11 +513,11 @@ def get(  # noqa: PLR0912, PLR0915
         # Might be good to put the rest of these checks into a separate function, so it can be called here and in the gather_data_array
         if self.ignore_errors:
             try:
-                data = self.gather_data_array(node)
+                data = node.data()
             except Exception:
                 return np.array()
         else:
-            data = self.gather_data_array(node)
+            data = node.data()
 
         logging.debug("Got data from tree.")
         if change_data:
@@ -519,39 +535,43 @@ def get(  # noqa: PLR0912, PLR0915
 
         return data
 
-    def gather_data_array(self, mds_node, dimension_names=None, dimension_units=None):
+    def get_xarray(self, get_call, np_data_type=np.float64, change_data=True, load_from_saved=True):
         """
-        Package data along with dimensions and attributes into an xarray DataArray. Pulls data from MDSPlus or local files.
+        Get data and dimensions from MDSplus tree, then store in an xarray along with metadata and proper dimensions as defined in the class
 
         Parameters
         ----------
-        mds_node : MDSPlus.node
-            mdsplus node to which desired data is attached
-        dimension_names : list[str]
-            list of human readable dimension names. Should be consistent with WiPPLPy conventions --insert a link here to some info about common WiPPLPy dimensions and conventions
-        dimension_units : list[str]
-            List of dimension units. Should be in a format consistent with astropy.units https://docs.astropy.org/en/stable/units/
+        get_call : str
+            A string that defines the call to use on the tree.
+        np_data_type : data-type, default=np.float64
+            The numpy data type to change the data to.
+        change_data : bool, default=True
+            Whether to change the data type of what MDSplus returns.
+        load_from_saved : bool, default=True
+            Whether to try to load the data from the saved calls.
 
         Returns
         -------
-        array : xr.DataArray
-            DataArray with stored data and metadata
-
+        data : xarray DataArray
+            The data from the tree packaged into an xarray
         """
-        # get data first as numpy array
 
-        data = mds_node.data()
-        num_dimensions = data.ndim
+        self.set_array_dimensions()
 
-        if num_dimensions != len(dimension_units):
-            raise Exception(
-                "*** Number of dimension names and number of dimension units does not match"
-            )
+        dimension_units = self.dimension_units
+        dimension_names = self.dimension_names
+        print(type(connection))
+        num_dimensions = connection
+        if isinstance(num_dimensions, list) and isinstance(dimension_names, list):
+            if num_dimensions != len(dimension_units):
+                raise Exception(
+                    "*** Number of dimension names and number of dimension units does not match"
+                )
 
-        if num_dimensions != len(dimension_names):
-            raise Exception(
-                "*** Number of dimension names and number of data dimensions does not match"
-            )
+            if num_dimensions != len(dimension_names):
+                raise Exception(
+                    "*** Number of dimension names and number of data dimensions does not match"
+                )
 
         coords = {}
         dimension_units = {}
@@ -559,11 +579,11 @@ def gather_data_array(self, mds_node, dimension_names=None, dimension_units=None
         for dim_num, dim_name in dimension_names:
             coords[dim_name] = data.dim_of(dim_num).data()
             dimension_units[dim_name] = dimension_units
-
+        print(type(mds_node)) #delete me
         coords["shot_num"] = mds_node.shot
 
         # get the rest of the attributes together into
-        attributes = {"units": dimension_units, "call_string": "thing", "version": 1.0}
+        attributes = {"units": dimension_units, "call_string": self.call_string, "version": 1.0}
 
         data_xarray = xr.DataArray(
             data, dims=dimension_names, coords=coords, attrs=attributes

From ec3897a6d804b892bc6f4ae5dff7e8484cd78f4a Mon Sep 17 00:00:00 2001
From: Ben Antognetti <antognetti@wisc.edu>
Date: Thu, 26 Jun 2025 14:28:48 -0500
Subject: [PATCH 11/12] First functioning Data class with xarray capability

---
 src/wipplpy/modules/generic_get_data.py | 67 ++++++++++++-------------
 1 file changed, 32 insertions(+), 35 deletions(-)

diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index 37eccb0..d67f6c9 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -217,6 +217,10 @@ def __init__(  # noqa: PLR0913
 
         self._tree = None
 
+        #Make attributes for dimension_names and dimension_units if specified
+        self.units=[]
+        self.names=[]
+
         # Initialize the time index range as empty and then try to get something for it. We do this because some code in _to_time_index_range requires it.
         self.time_index_range = None
         self.sample_period = sample_period
@@ -233,6 +237,8 @@ def __init__(  # noqa: PLR0913
         elif len(get_calls) == 0:
             logging.info("Did not do any get calls for preloading data into object.")
 
+        self.get_calls = get_calls
+
         # Hold all the calls and call data gotten from MDSplus.
         # TODO: Change how calls are saved so that we can change loaded attributes and save the update.
         self.saved_calls = {}
@@ -333,20 +339,6 @@ def _to_time_index(self, time):
 
         return index
 
-    def set_array_dimensions(self):
-        """
-        Function to be overwrriten when Data class is implemented for a specific data set
-
-        Parameters
-        ----------
-        dimension_names : list[str]
-            list of human readable dimension names. Should be consistent with WiPPLPy conventions --insert a link here to some info about common WiPPLPy dimensions and conventions--
-        dimension_units : list[str]
-            List of dimension units. Should be in a format consistent with astropy.units https://docs.astropy.org/en/stable/units/
-        """
-        self.dimension_units=[]
-        self.dimension_names=[]
-
     def _get_individuals(self, variable_booleans, get_calls):
         """
         Get all data that has a True boolean associated with it.
@@ -535,7 +527,7 @@ def get(  # noqa: PLR0912, PLR0915
 
         return data
 
-    def get_xarray(self, get_call, np_data_type=np.float64, change_data=True, load_from_saved=True):
+    def get_xarray(self, np_data_type=np.float64, change_data=True, load_from_saved=True):
         """
         Get data and dimensions from MDSplus tree, then store in an xarray along with metadata and proper dimensions as defined in the class
 
@@ -555,42 +547,47 @@ def get_xarray(self, get_call, np_data_type=np.float64, change_data=True, load_f
         data : xarray DataArray
             The data from the tree packaged into an xarray
         """
+        
+        units = self.units
+        names = self.names
+        get_call = self.get_calls[0]
+        print(get_call)
 
-        self.set_array_dimensions()
-
-        dimension_units = self.dimension_units
-        dimension_names = self.dimension_names
-        print(type(connection))
-        num_dimensions = connection
-        if isinstance(num_dimensions, list) and isinstance(dimension_names, list):
-            if num_dimensions != len(dimension_units):
+        #Needs to get expanded for multiple get_calls passed!!!!!!!!!!!!!&&&&&&&&&&&&&&&&&&&)))))))()()()
+        
+        data = self.get(get_call, np_data_type=np_data_type, change_data=change_data, load_from_saved=load_from_saved)
+        
+        num_dimensions = data.ndim
+        if isinstance(units, list) and isinstance(names, list):
+            if num_dimensions + 1 != len(units):
                 raise Exception(
                     "*** Number of dimension names and number of dimension units does not match"
                 )
 
-            if num_dimensions != len(dimension_names):
+            if num_dimensions + 1 != len(names):
                 raise Exception(
                     "*** Number of dimension names and number of data dimensions does not match"
                 )
 
-        coords = {}
-        dimension_units = {}
+        coords_dict = {}
+        units_dict = {}
+
+        for dim_num, dim_name in enumerate(names[1:]):
+            coords_dict[dim_name] = self.get('DIM_OF('+ get_call + ', {:d})'.format(dim_num), np_data_type=np_data_type, change_data=change_data, load_from_saved=load_from_saved)
+            units_dict[dim_name] = units[dim_num+1]
 
-        for dim_num, dim_name in dimension_names:
-            coords[dim_name] = data.dim_of(dim_num).data()
-            dimension_units[dim_name] = dimension_units
-        print(type(mds_node)) #delete me
-        coords["shot_num"] = mds_node.shot
+        units_dict[names[0]] = units[0]
+        
+        coords_dict["shot_num"] = int(self.get('$SHOT'))
 
         # get the rest of the attributes together into
-        attributes = {"units": dimension_units, "call_string": self.call_string, "version": 1.0}
+        attributes = {"units": units_dict, "call_string": get_call, "version": 1.0, 'tree': self.get('$EXPT', change_data = False)}
 
         data_xarray = xr.DataArray(
-            data, dims=dimension_names, coords=coords, attrs=attributes
+            data, dims=names[1:], coords=coords_dict, attrs=attributes
         )
 
-        self.xarray = data_xarray  # hmm which one
-        return data_xarray
+        self.xarray = data_xarray  
 
     def to_raw_index(self, time_index):
         """

From 80f111e6c6e054c0f5109a0b8f26780a5a3c4db9 Mon Sep 17 00:00:00 2001
From: Ben Antognetti <antognetti@wisc.edu>
Date: Fri, 27 Jun 2025 15:07:12 -0500
Subject: [PATCH 12/12] Added first example of diagnostic definition

---
 src/wipplpy/__init__.py                 |  1 +
 src/wipplpy/modules/generic_get_data.py |  2 +-
 src/wipplpy/mst/diagnostics/summary.py  | 24 ++++++++++++++++++++++++
 3 files changed, 26 insertions(+), 1 deletion(-)
 create mode 100644 src/wipplpy/mst/diagnostics/summary.py

diff --git a/src/wipplpy/__init__.py b/src/wipplpy/__init__.py
index 37579ee..66a65b3 100644
--- a/src/wipplpy/__init__.py
+++ b/src/wipplpy/__init__.py
@@ -8,3 +8,4 @@
 ]
 
 from wipplpy import modules
+from .mst.diagnostics.summary import PlasmaCurrent
\ No newline at end of file
diff --git a/src/wipplpy/modules/generic_get_data.py b/src/wipplpy/modules/generic_get_data.py
index d67f6c9..f8a8783 100644
--- a/src/wipplpy/modules/generic_get_data.py
+++ b/src/wipplpy/modules/generic_get_data.py
@@ -167,7 +167,7 @@ def __init__(  # noqa: PLR0913
     ):
         """
         Generic class for dealing with data from a remote MDSplus database.
-
+ 
         Parameters
         ----------
         tree : Connection or int
diff --git a/src/wipplpy/mst/diagnostics/summary.py b/src/wipplpy/mst/diagnostics/summary.py
new file mode 100644
index 0000000..8fd9aa7
--- /dev/null
+++ b/src/wipplpy/mst/diagnostics/summary.py
@@ -0,0 +1,24 @@
+import matplotlib.pyplot as plt
+from wipplpy.modules.generic_get_data import Data as Data
+import numpy as np
+import xarray as xr
+import MDSplus as mds
+
+class PlasmaCurrent(Data):
+    def __init__(self, tree):
+            #Ordering does matter. Define calls, super init, then dimension specifications. Figuring out how to make it not matter, or streamline whats needed would be cool
+            calls = ['\MST_OPS::IP_F'] #want to add ability to have multiple in this list
+            super().__init__(tree, [True], calls) # could augment second argument as a keyword with Default None in which case it does all of calls
+            self.units = ['kA', 's']
+            self.names = ['plasma_current', 'shot_time']
+
+    def plot(self):
+        if not hasattr(self, "xarray"):
+            self.get_xarray()
+            print("Put together xarray")
+
+        fig, ax = plt.subplots(figsize=(8,4))
+        plt.plot(self.xarray.shot_time * 1000, self.xarray.data)
+        ax.set_xlabel('Time (ms)')
+        ax.set_ylabel('Plasma Current (kA)')
+        plt.show()
\ No newline at end of file