177 finish kalman tutorial

doc/README.md

@@ -4,7 +4,7 @@
 
 ## Start Here
 
-[Tutorial](tutorial.md) : Steps through installation, running, updating configuration files, and loading plugins. IN PROGRESS
+[Tutorial](tutorial.md) : Steps through installation, running, updating configuration files, loading plugins, and writting your own plugin.
 
 [Purpose and Use](purpose-and-use.md) : When to use OnAIR (and when _not_ to). NOT COMPLETE
 
@@ -16,8 +16,6 @@
 
 [Unit-Testing](unit-testing.md) : How to run the unit-tests and generate a coverage report.
 
-[Writing your own Plugin](writing-your-own-plugin.md) : NOT COMPLETE
-
 [Writing your own DataSource](writing-your-own-data-source.md) : NOT COMPLETE
 
 ## Further Reading/Learning

doc/tutorial.md

@@ -131,3 +131,274 @@ ComplexPluginDict = {'generic':'plugins/generic/__init__.py'}
 ```
 
 ## Tutorial: Using the Kalman Plugin
+
+In the default configuration, OnAIR doesn't do any processing of the data.
+Now, we'll take a look at the Kalman example which processes frames of data with a Kalman Filter ([wikipedia: Kalman Filter(https://en.wikipedia.org/wiki/Kalman_filter), [PyPI: simdkalman](https://pypi.org/project/simdkalman/)) in one plugin and outputs the results to a file using a second plugin.
+
+### Kalman Configuration
+
+The Kalman example configuration [kalman_csv_output_example.ini](../onair/config/kalman_csv_output_example.ini) has the following listed for Plugins:
+
+```
+[PLUGINS]
+KnowledgeRepPluginDict = {'Kalman Filter': 'plugins/kalman'}
+LearnersPluginDict = {'csv output':'plugins/csv_output'}
+PlannersPluginDict = {}
+ComplexPluginDict = {}
+```
+
+Note: you can set plugins to be blank or the 'generic' empty plugin.
+
+You can see that there is now a KnowledgeRep plugin, Kalman Filter: this plugin will see the low-level data frame and use it to build up higher level information.
+In this case, a list of telemetry points that have violated their Kalman filter prediction for a time step.
+There is also a Learners plugin, csv output: normally a learner would use both the low-level data and the higher level information from the Knowledge Representation to TODO.
+In this example we want the csv output plugin to see both the Kalman filter output and the low level data so that it can be written to a file.
+
+The image below shows the data flow from a csv file, into OnAIR, into the plugins (in yellow), and back out to csv files:
+
+![](images/kalman_onair_example.png)
+
+### Inside the Kalman Plugin
+
+The Kalman Plugin [kalman_plugin.py](../onair/plugins/kalman/kalman_plugin.py) is an [`AIPlugin`](../onair/src/ai_components/ai_plugin_abstract/ai_plugin.py) which requires two functions: `update` and `render_reasoning`.
+`AIPlugin` also defines an `__init__` function which stores the plugin name and a list of names of the telemetry points in the low level data (called "headers").
+
+The `update` function is how the plugin recieves each new data frame:
+
+```
+    def update(self, low_level_data=None, _high_level_data=None):
+        """
+        Update the frames with new low-level data.
+
+        This method converts the input data to float type, appends it to the
+        corresponding frames, and maintains the window size by removing older
+        data points if necessary.
+
+        Parameters
+        ----------
+        low_level_data : list
+            Input sequence of data points with length equal header dimensions.
+
+        Returns
+        -------
+        None
+        """
+        if low_level_data is None:
+            print_msg(
+                "Kalman plugin requires low_level_data but received None.", ["FAIL"]
+            )
+        else:
+            frame = floatify_input(low_level_data)
+
+            for i, value in enumerate(frame):
+                self.frames[i].append(value)
+                if len(self.frames[i]) > self.window_size:
+                    self.frames[i].pop(0)
+```
+
+This plugin simply stores the new data frame alongside a sliding window of previous data frames.
+The data frames are actually processed in the `render_reasoning` function:
+
+```
+    def render_reasoning(self):
+        """
+        Generate a list of attributes that show fault-like behavior based on residual analysis.
+
+        This method calculates residuals using the Kalman filter predictions and compares
+        them against a threshold. Attributes with residuals exceeding the threshold are
+        considered to show fault-like behavior, except for the 'TIME' attribute.
+
+        Returns
+        -------
+        list of str
+            A list of attribute names that show fault-like behavior (i.e., have residuals
+            above the threshold). The 'TIME' attribute is excluded from this list even
+            if its residual is above the threshold.
+
+        Notes
+        -----
+        The residual threshold is defined by the `residual_threshold` attribute of the class.
+        """
+        residuals = self._generate_residuals()
+        residuals_above_thresh = residuals > self.residual_threshold
+        broken_attributes = []
+        for attribute_index in range(len(self.frames)):
+            if (
+                residuals_above_thresh[attribute_index]
+                and not self.headers[attribute_index].upper() == "TIME"
+            ):
+                broken_attributes.append(self.headers[attribute_index])
+        return broken_attributes
+```
+
+The output of `render_reasoning` is a list that is passed to later plugins as high level data; the Kalman Plugin reports which telemetry points it has flagged as broken (e.g. out of the expected bounds of the Kalman filter's prediction).
+This way you can build chains of more complicated behavior as plugins build on the results of earlier plugins while isolating specific functionality.
+For example, you could write a plugin that attempts to diagnose faults based on what telemetry points have been flagged as broken by the Kalman filter and/or other fault detection algorithms.
+
+### Output
+
+Run the Kalman example with `python driver.py onair/config/kalman_csv_output_example.ini`.
+The terminal should show similar output as the default run, but probably a little slower as OnAIR is actually doing something now.
+
+The run should generate a file named `csv_out_[date/time].csv (the data/time is in the format of day of year, hour, minute).
+It may generate multiple files if the execution spans multiple minutes.
+This file has all of the data that was visible to the csv output plugin: low level data and the high level output from the Kalman plugin.
+
+For most of the output, the Kalman plugin didn't flag any telemetry points as broken (which is good!).
+This particular data file was generated with jumps in the current, so you should see some lines such as:
+
+```
+> cat cat csv_out_323_21_57.csv
+--- snip ---
+946689342.0,18.0,5.0,200.0,1834.2,2.46,43.76,0.0,0.0
+946689343.0,18.0,5.0,200.0,1836.06,1.72,43.65,0.0,0.0
+946689344.0,18.0,5.0,200.0,1837.82,1.52,43.55,0.0,0.0
+946689345.0,18.0,2.0,200.0,1839.95,2.26,43.43,0.0,1.0,CURRENT
+946689346.0,18.0,2.0,200.0,1841.78,1.66,43.33,0.0,1.0
+946689347.0,18.0,3.0,200.0,1843.55,1.55,43.23,0.0,1.0
+946689348.0,18.0,3.0,200.0,1845.57,2.05,43.11,0.0,1.0
+946689349.0,18.0,5.0,200.0,1847.68,2.22,42.99,0.0,0.0,CURRENT
+946689350.0,18.0,5.0,200.0,1849.88,2.41,42.86,0.0,0.0
+946689351.0,18.0,5.0,200.0,1851.73,1.7,42.76,0.0,0.0
+946689352.0,18.0,5.0,200.0,1853.62,1.79,42.65,0.0,0.0
+--- snip ---
+```
+
+Here you see that the 3rd column (CURRENT) is steady at 5.0.
+When it drops to 2.0, "CURRENT" is added to the output from the Kalman plugin.
+This happens again when the current jumps again from 3.0 to 5.0.
+
+Note: not every telemetry point flagged by the Kalman filter is idicative of a fault, some are false positives.
+
+## Write a New Plugin
+
+Now we are going to write a new plugin to "scream" every time a tlemetry point has been marked as broken by the Kalman plugin.
+
+First we need to create a directory and files for the plugin.
+The easiest way to do this is to just copy the generic plugin directory.
+Note: the plugin directory can be placed anywhere; you just have to update your configuration (.ini) file with the correct location.
+I will keep things in the plugin directory to make this simple, but you may not want to mix the your custom plugin source code with the rest of OnAIR's code.
+
+```
+- from top level OnAIR directory -
+> cd plugins
+> cp -r generic scream
+> mv scream/generic_plugin.py scream/scream_plugin.py
+```
+
+Create a new configuration file; we'll base ours off of the Kalman example we just used.
+
+```
+- from top level OnAIR directory -
+> cd onair/config
+> cp kalman_csv_output_example.ini scream_example.ini
+```
+
+Now edit `scream_example.ini` to have a Complex Reasoner plugin by changing this:
+
+```
+ComplexPluginDict = {}
+```
+
+to this:
+
+```
+ComplexPluginDict = {'Scream': 'plugins/scream'}
+```
+
+Run OnAIR with your new config to confirm that there are no errors (behavior should be the same as the Kalman example since your new plugin doesn't do anything yet).
+
+Now edit `scream_example.py`:
+
+```
+from onair.src.ai_components.ai_plugin_abstract.ai_plugin import AIPlugin
+
+
+class Plugin(AIPlugin):
+    def update(self, low_level_data=[], high_level_data={}):
+        """
+        Given streamed data point, system should update internally
+        """
+        if not 'Kalman Filter' in high_level_data['vehicle_rep']:
+            print("No 'Kalman Filter' plugin! Scream has nothing to scream about.")
+        else:
+            broken_telemetry_points = high_level_data['vehicle_rep']['Kalman Filter']
+            if len(broken_telemetry_points) > 0:
+                print("AHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH")
+                print("Everything is messed up! Specifically:")
+                print(broken_telemetry_points)
+                print("AHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH")
+
+    def render_reasoning(self):
+        """
+        System should return its diagnosis
+        """
+        pass
+```
+
+We do everything in the `update` function since scream doesn't actually have anything useful to pass on to other plugins.
+First we check that the high level data does in fact have an entry named "Kalman Filter", which is the name of the Kalman plugin in the config file.
+
+Next, the plugin checks the Kalman plugins rendered output (`high_level_data['vehicle_rep']['Kalman Filter']` is the list returned by the Kalman plugin's `render_reasoning` function).
+If something is there, the scream plugin will, well scream about it.
+
+When you run your scream example, you should now see the following amoung the output:
+
+```
+--- snip ---
+
+--------------------- STEP 943 ---------------------
+
+CURRENT DATA: [946689342.0, 18.0, 5.0, 200.0, 1834.2, 2.46, 43.76, 0.0, 0.0]
+INTERPRETED SYSTEM STATUS: ---
+
+--------------------- STEP 944 ---------------------
+
+CURRENT DATA: [946689343.0, 18.0, 5.0, 200.0, 1836.06, 1.72, 43.65, 0.0, 0.0]
+INTERPRETED SYSTEM STATUS: ---
+
+--------------------- STEP 945 ---------------------
+
+CURRENT DATA: [946689344.0, 18.0, 5.0, 200.0, 1837.82, 1.52, 43.55, 0.0, 0.0]
+INTERPRETED SYSTEM STATUS: ---
+AHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+Everything is messed up! Specifically:
+['CURRENT']
+AHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+
+--------------------- STEP 946 ---------------------
+
+CURRENT DATA: [946689345.0, 18.0, 2.0, 200.0, 1839.95, 2.26, 43.43, 0.0, 1.0]
+INTERPRETED SYSTEM STATUS: ---
+
+--------------------- STEP 947 ---------------------
+
+CURRENT DATA: [946689346.0, 18.0, 2.0, 200.0, 1841.78, 1.66, 43.33, 0.0, 1.0]
+INTERPRETED SYSTEM STATUS: ---
+
+--------------------- STEP 948 ---------------------
+
+CURRENT DATA: [946689347.0, 18.0, 3.0, 200.0, 1843.55, 1.55, 43.23, 0.0, 1.0]
+INTERPRETED SYSTEM STATUS: ---
+
+--------------------- STEP 949 ---------------------
+
+CURRENT DATA: [946689348.0, 18.0, 3.0, 200.0, 1845.57, 2.05, 43.11, 0.0, 1.0]
+INTERPRETED SYSTEM STATUS: ---
+AHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+Everything is messed up! Specifically:
+['CURRENT']
+AHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+
+--------------------- STEP 950 ---------------------
+
+CURRENT DATA: [946689349.0, 18.0, 5.0, 200.0, 1847.68, 2.22, 42.99, 0.0, 0.0]
+INTERPRETED SYSTEM STATUS: ---
+
+--------------------- STEP 951 ---------------------
+
+CURRENT DATA: [946689350.0, 18.0, 5.0, 200.0, 1849.88, 2.41, 42.86, 0.0, 0.0]
+INTERPRETED SYSTEM STATUS: ---
+
+--- snip ---
+```

onair/config/kalman_csv_output_example.ini

@@ -1,6 +1,6 @@
 [FILES]
 TelemetryFilePath = onair/data/raw_telemetry_data/data_physics_generation/Errors
-TelemetryFile = 700_crash_to_earth_1.csv
+TelemetryFile = 1600_current_jump_3.csv
 MetaFilePath = onair/data/telemetry_configs/
 MetaFile = data_physics_generation_CONFIG.json