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updates for release 0.8.2
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gutow committed Jul 10, 2024
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3 changes: 2 additions & 1 deletion docs/Change_Log.md
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# Change Log
* * X.X.X (July, X, 2024)
* 0.8.2 (July, 10, 2024)
* BUG FIX: Increased checking to avoid javascript errors in Jupyter Lab
and Notebook >= 7, while maintaining NBClassic capabilities.
* Documentation updates and improvements.
* 0.8.1 (May 2, 2023)
* BUG FIX: Now always waits for all data to be transferred to plot before
writing backup to a file.
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14 changes: 7 additions & 7 deletions docs/Installation.md
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Expand Up @@ -129,16 +129,16 @@ Python](https://docs.python-guide.org/dev/virtualenvs/).
https://cms.gutow.uwosh.edu/Gutow/useful-chemistry-links/software-tools-and-coding/computer-and-coding-how-tos/installing-jupyter-on-raspberrian)
for a discussion of adding swap space on a Pi.
6. Still within the environment shell test
this by starting jupyter `jupyter notebook` or `jupyter lab`. Jupyter should
launch in your browser.
this by starting jupyter `jupyter notebook`, `jupyter lab` or `jupyter
nbclassic`. Jupyter should launch in your browser.
1. Open a new notebook using the default (Python 3) kernel.
2. In the first cell import all from DAQinstance.py:
`from jupyterpidaq.DAQinstance import *`.
When run in jupyter notebook this cell should load the DAQmenu at the
end of the Jupyter notebook menu/icon bar. Currently, no convenience
menu is available in Jupyter lab. If you do not have an appropriate
A-to-D board installed you will get a message and the software
will default to demo mode, substituting a random number
In classic notebook this cell should load the DAQmenu at the
end of the Jupyter notebook menu/icon bar. In Notebook and Lab DAQ
Commands menu should appear on launch of Jupyter. If you do not
have an appropriate A-to-D board installed you will get a message and
the software will default to demo mode, substituting a random number
generator for the A-to-D.
7. If you wish, you can make this environment available to an alternate Jupyter
install as a special kernel when you are the user.
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83 changes: 43 additions & 40 deletions docs/User_Guide.md
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Expand Up @@ -42,8 +42,9 @@ up, that lead to slightly different steps for starting the software:
[Installation Instructions](https://jupyterphysscilab.github.io/JupyterPiDAQ/jupyterpidaq.html#installation)).
* In this case launch
Jupyter, in whichever directory you want to work, using the
command: `jupyter nbclassic` (for the old notebook interface) or `jupyter
lab` (for the newer lab interface).
command: `jupyter lab` (for the newer lab interface), `jupyter notebook`
(for the modern notebook interface), or `jupyter nbclassic` (for the old
notebook interface).
* Open a new notebook and choose the kernel
for `JupyterPiDAQ`. The kernel name will depend upon what was chosen
during installation.
Expand All @@ -52,25 +53,29 @@ up, that lead to slightly different steps for starting the software:
* In this case you must navigate to the
directory of the virtual environment using the `cd` command before
starting the software.
* Then enter the virtual environment with the command `pipenv shell`.
This assumes you set up `pipenv` as described in the
[Installation instructions](https://jupyterphysscilab.github.io/JupyterPiDAQ/jupyterpidaq.html#installation).
* Launch Jupyter using the command: `jupyter nbclassic` (for the old
notebook interface) or `jupyter lab` (for the newer lab interface).
* Then enter the virtual environment with the command `pipenv shell` (you
might be using `venv` or something else). This assumes you set up
`pipenv` as described in the [Installation instructions
](https://jupyterphysscilab.github.io/JupyterPiDAQ/jupyterpidaq.html#installation).
* Launch Jupyter using the
command: `jupyter lab` (for the newer lab interface), `jupyter notebook`
(for the modern notebook interface), or `jupyter nbclassic` (for the old
notebook interface).
* Open a new python notebook.

### Initialize the Data Acquisition Tools

Initialize the data acquisition tools by putting the statement `from
jupyterpidaq.DAQinstance import *` into the first cell and clicking on the
'Run' button. The package loads supporting packages (numpy, pandas, plotly,
etc...) and searches for compatible hardware. On a Raspberry Pi this takes a
number of seconds. If no compatible A-to-D boards are found, demo mode is used.
In demo mode the A-to-D board is simulated by a random number generator.
jupyterpidaq.DAQinstance import *` into the first cell and then running
(executing) the cell. The package loads supporting packages (numpy, pandas,
plotly, etc...) and searches for compatible hardware. On a Raspberry Pi this
takes a number of seconds. If no compatible A-to-D boards are found, demo
mode is used. In demo mode the A-to-D board is simulated by a random number
generator.

When setup is done a new menu appears at the end of the menubar (figure 1).

![DAQ Menu](DAQmenu.png)
![DAQ Menu](https://jupyterphysscilab.github.io/JupyterPiDAQ/DAQmenu.png)

**Figure 1**: The menu created once the data acquisition software is
initialized. Currently NOT available in Jupyter Lab.
Expand All @@ -82,11 +87,10 @@ a new column in a DataFrame, or fitting data.
### Collecting data
**Using the Menu**

From the "DAQ Commands" menu select "Insert New Run After Selection..." or
"Append New Run to End...". The first will insert the code to set up
data collection for a run in the cell below the currently selected cell.
The second will append this to the end of the notebook. When the cell is
run it will generate
From the "DAQ Commands" menu select "Insert New run after selected cell..."
This will insert the code to set up data collection for a run in the cell
below the currently selected cell. Insert the name you want for the run
into the code as specified. When the cell is run it will generate
a GUI that looks like the figure 2, below. Fill in the information to define
what you wish to do (see below figure 2 for more details).

Expand All @@ -98,10 +102,10 @@ string you want for this run. Replacing spaces with _ will prevent issues,
especially on Windows. After entering the command, run the cell. This will
generate the GUI shown in figure 2.

<img src="newrun.png" alt="New Run Figure" style="width:100%;">
<img src="https://jupyterphysscilab.github.io/JupyterPiDAQ/newrun.png" alt="New Run Figure" style="width:100%;">

**Figure 2**: Image of the GUI for setting up a data collection run.
1. Give the run a title/name using the first textbox.
1. You can give the run a different title/name using the first textbox.
2. You can collect up to four (4) data traces at once. Two different data
traces can display the same analog-to-digital channel, but in different
units (e.g. you could record both the raw voltage and temperature from a
Expand Down Expand Up @@ -135,21 +139,20 @@ generate the GUI shown in figure 2.

#### In a table

Selecting the "Show data in table..." option in the "DAQ Command" menu will
insert a cell immediately below the currently selected cell displaying a
widget in which you can select which data set to display. The command
equivalent is `showDataTable()`.
Selecting the "Select data to show in a table..." option in the "DAQ
Command" menu will insert a cell immediately below the currently selected
cell displaying a widget in which you can select which data set to display.
The command equivalent is `showDataTable()`.

#### Plotting data

Selecting the "Insert new plot after selection..." option in the menu will
insert two cells immediately below the currently selected cell. The first cell
will be used to generate a GUI to lead you through creation of the code to
generate the plot. The second cell is where the plot creation code is
generated. The first tab of this GUI looks like figure 3. The command
equivalent is `newPlot()`.
Selecting the "Insert new plot after selected cell" option in the menu will
insert a cell immediately below the currently selected cell. This will
create a GUI to lead you through generating code to make a plot of a data
set. The code is generated immediately below the GUI. The first tab of this GUI
looks like figure 3. The command equivalent is `newPlot()`.

![Plot GUI](plot_GUI.png)
![Plot GUI](https://jupyterphysscilab.github.io/JupyterPiDAQ/plot_GUI.png)

**Figure 3**: Image of the first tab in the four tab (4 step) Pandas Plot
Composer. More information in the [Pandas_GUI
Expand All @@ -170,13 +173,13 @@ The GUI destroys itself once you complete step 4.

#### Calculating a new column

Selecting "Calculate new column..." from the menu will add two cells
immediately below the selected cell. The first cell will create the GUI to
lead you through creation of the code to calculate the new column. The second
cell is where the code is built. The first tab of the GUI looks like
Selecting "Calculate new column..." from the menu will a cell
immediately below the selected cell and launch the GUI to
lead you through creation of the code to calculate the new column. The code
is created immediately below the GUI. The first tab of the GUI looks like
figure 4. The command equivalent is `newCalculatedColumn()`.

![New Column GUI](new_col_GUI.png)
![New Column GUI](https://jupyterphysscilab.github.io/JupyterPiDAQ/new_col_GUI.png)

**Figure 4**: Image of the first tab in the four tab (4 step) Pandas New
Calculated Column Composer. More information in the [Pandas_GUI
Expand All @@ -190,12 +193,12 @@ The GUI destroys itself once you complete step 4.
#### Fitting data

A GUI for defining simple fits (linear, polynomial, exponential decay, sine
and Gaussian) can be launched by selecting "Insert new Fit after selection..
." from the menu. This will create the GUI to lead you through selecting
and fitting the data. The code is created in the cell immediately below the
and Gaussian) can be launched by selecting "Insert new fit after selected
cell" from the menu. This will create the GUI to lead you through selecting
and fitting the data. The code is created the immediately below the
GUI. The command equivalent is `newFit()`.

![Fit Pandas GUI](fit_gaussian_tab1.png)
![Fit Pandas GUI](https://jupyterphysscilab.github.io/JupyterPiDAQ/fit_gaussian_tab1.png)

**Figure 5**: Image of the first tab in the Pandas Fit Composer.
More information in the [Pandas_GUI
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