add flow chart for workflow

Author: PaulHancock

docs/source/introduction.md

@@ -2,21 +2,23 @@
 
 Robbie automates the process of cataloguing sources, finding variables, and identifying transients.
 
-The workflow is described in [Hancock et al. 2018](https://ui.adsabs.harvard.edu/abs/2019A%26C....27...23H/abstract) and carries out the following steps:
+The workflow was described initially in [Hancock et al. 2018](https://ui.adsabs.harvard.edu/abs/2019A%26C....27...23H/abstract) however the current workflow is shown below:
 - Preprocessing:
-  - Find sources in images
-  - Compare these catalogues to a reference catalogue
-  - Use the offsets to model image based distortions
-  - Make warped/corrected images
-- Persistent source catalogue creation:
-  - Stack the warped images into a cube and form a mean image
-  - Source find on the mean image to make a master catalogue
+  - Convolve all images to a common psf (optional)
+  - Create background and noise maps (if they are not found)
+  - Correct astrometry using fitswarp (optional)
+- Variabile/persistent source detection:
+  - Stack the warped images to form a mean image
+  - Source find on the mean image to make a reference catalogue
   - Priorized fit this catalogue into each of the individual images
-  - Join the catalogues into a single table and calculate variability stats
+  - Join the epoch catalogues to make a persistent source catalogue
+  - Calculate variability stats and generate a light curve for each source
 - Transient candidate identification:
-  - Use the persistent source to mask known sources from the individual images
-  - Source find on the masked images to look for transients
-  - Combine transients tables into a single catalogue, identifying the epoch of each detection
+  - Use the persistent source to mask known sources from the individual epochs
+  - Source find on the masked images to find transients
+  - Concatenate transients into a single catalogue, identifying the epoch of each detection
+
+See [workflow](workflow) for a diagram of how Robbie works.
 
 ## Dependencies
 Robbie relies on the following software:

docs/source/workflow.md

@@ -0,0 +1,45 @@
+(workflow)=
+## Workflow
+The workflow was described initially in [Hancock et al. 2018](https://ui.adsabs.harvard.edu/abs/2019A%26C....27...23H/abstract) however the current workflow is shown below:
+- Preprocessing:
+  - Convolve all images to a common psf (optional)
+  - Create background and noise maps (if they are not found)
+  - Correct astrometry using fitswarp (optional)
+- Variabile/persistent source detection:
+  - Stack the warped images to form a mean image
+  - Source find on the mean image to make a reference catalogue
+  - Priorized fit this catalogue into each of the individual images
+  - Join the epoch catalogues to make a persistent source catalogue
+  - Calculate variability stats and generate a light curve for each source
+- Transient candidate identification:
+  - Use the persistent source to mask known sources from the individual epochs
+  - Source find on the masked images to find transients
+  - Concatenate transients into a single catalogue, identifying the epoch of each detection
+
+
+```mermaid
+flowchart TD
+  subgraph Preprocessing
+    direction LR
+    img[Raw images] --> psf["PSF correction (?)"]
+    psf --> bkg[Create background/noise maps]
+    bkg --> warp["Fits warping (?)"]
+    warp --> epim[Epoch images]
+  end
+  subgraph Persistent sources
+    epim --> mean[Mean image]
+    mean --> pscat[Persistent sources]
+    epim --> pscat
+    pscat --> vout[(Flux table, variability table, light curves, variabiltiy plot)]
+  end
+  subgraph Transients
+    mean --> mask[Masked epoch images]
+    epim --> mask
+    pscat --> mask
+    mask --> trans[Transient candidates]
+    trans --> tout[(Filtered candidates, transients plot)]
+  end
+```
+
+Items with a (?) are optional processing steps that can be turned on/off.
+Items in a cylinder are the final outputs of the processing workflow.