From 7ccf0fc9baea563964275fca38472e077b6ef522 Mon Sep 17 00:00:00 2001
From: Parv Agarwal <65726543+Parvfect@users.noreply.github.com>
Date: Sun, 16 Oct 2022 20:31:18 +0100
Subject: [PATCH] Adding pipelines for cli analysis (#202)
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* started pipelines function

* almost working simple function equivalents of nb scripts

* fix: fixed import (brainflow updated API)

* sqc fixes for unicorn (#176)

* Ignore pushes

* Trying to create a cli

* Stepping through the problem

* First commit

* Fixing pause in signal quality check

* Fixing Signal quality check problem

* fix the technical debt

* Save path done for automated saving pdf

* I feel amazing

* Almost through

* Update eegnb/cli/__main__.py

Co-authored-by: Erik Bjäreholt <erik@bjareho.lt>

* Trying to create cli but it's being really painful

* Extra word cli error

* Changed example handling

* Pain

* Adding whole datapath

* Finally fixed cli

* hmm

* Looking good

* added hyperlink

* Having some issues with detecting css and image deltetion

* Just the css now

* Fixed the css linking problem though it's a weird soln

* Automated running, still fnames problem

* Hahahah embedded images in html

* Improving code

* Okay now

* Look at that

* Almost there just the two figures now

* Now

* Added attrdict to do with cli error

Co-authored-by: John Griffiths <j.davidgriffiths@gmail.com>
Co-authored-by: Erik Bjäreholt <erik@bjareho.lt>
Co-authored-by: John Griffiths <JohnGriffiths@users.noreply.github.com>
---
 eegnb/cli/__main__.py    | 31 ++++++++++++++++++++++
 eegnb/cli/introprompt.py | 57 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 88 insertions(+)

diff --git a/eegnb/cli/__main__.py b/eegnb/cli/__main__.py
index d43702e4..e9ddc9ce 100644
--- a/eegnb/cli/__main__.py
+++ b/eegnb/cli/__main__.py
@@ -128,6 +128,37 @@ def create_analysis_report(
             experiment, eegdevice, subject, session, site, filepath = analysis_intro_prompt()
     analysis_report(experiment, eegdevice, subject, session, site, filepath)
 
+@main.command()
+@click.option("-ex", "--experiment", help="Experiment to run")
+@click.option("-ed", "--eegdevice", help="EEG device to use")
+@click.option("-sub", "--subject", help="Subject ID")
+@click.option("-sess", "--session", help="Session number")
+@click.option("-fp", "--filepath", help="Filepath to save data")
+@click.option(
+    "-ip", "--prompt", help="Use interactive prompt to ask for parameters", is_flag=True
+)
+def create_analysis_report(
+    experiment: str,
+    eegdevice: str = None,
+    subject: str = None, 
+    session: str = None,
+    filepath:str = None,
+    prompt: bool = False,
+):
+    """
+    Create analysis report of recorded data
+    """
+    
+    if prompt:
+        example = input("Do you want to load an example experiment? (y/n)\n")
+        print()
+        if example == 'y':
+            example_analysis_report()
+            return
+        else:
+            experiment, eegdevice, subject, session, filepath = analysis_intro_prompt()
+    create_analysis_report_(experiment, eegdevice, subject, session, filepath)
+
 
 @main.command()
 @click.option("-ed", "--eegdevice", help="EEG device to use", required=True)
diff --git a/eegnb/cli/introprompt.py b/eegnb/cli/introprompt.py
index 6f8aa488..cd9f7bbc 100644
--- a/eegnb/cli/introprompt.py
+++ b/eegnb/cli/introprompt.py
@@ -160,6 +160,63 @@ def intro_prompt() -> Tuple[EEG, str, int, str]:
 
     return eeg_device, exp_selection, duration, str(save_fn)
 
+def analysis_device_prompt():
+   
+    boards = {
+        "none": "None",
+        "muse2016": "Muse (2016)",
+        "muse2": "Muse 2",
+        "museS": "Muse S",
+        "muse2016_bfn": "Muse 2016 - brainflow, native bluetooth",
+        "muse2016_bfb": "Muse 2016 - brainflow, BLED bluetooth dongle",        
+        "muse2_bfn": "Muse 2 - brainflow, native bluetooth",
+        "muse2_bfb": "Muse 2 - brainflow, BLED bluetooth dongle",
+        "museS_bfn": "Muse S - brainflow, native bluetooth",
+        "museS_bfb": "Muse S - brainflow, BLED bluetooth dongle",
+        "ganglion": "OpenBCI Ganglion",
+        "cyton": "OpenBCI Cyton",
+        "cyton_daisy": "OpenBCI Cyton + Daisy",
+        "unicorn": "G.Tec Unicorn",
+        "brainbit": "BrainBit",
+        "notion1": "Notion 1",
+        "notion2": "Notion 2",
+        "crown": "Crown",
+        "synthetic": "Synthetic",
+        "freeeeg32": "FreeEEG32",
+    }
+
+    print("Please enter the integer value corresponding to your EEG device: \n")
+    print("\n".join(f"[{i:2}] {board}" for i, board in enumerate(boards.values())))
+
+    board_idx = int(input("\nEnter Board Selection: \n"))
+
+    # Board_codes are the actual names to be passed to the EEG class
+    board_code = list(boards.keys())[board_idx]
+    return board_code
+
+def analysis_intro_prompt():
+
+    # check if user has filepath
+    print("Welcome to NeurotechX EEG Notebooks\n")
+    print("Do you have a filepath to a .csv file you would like to analyze? \n")
+    print("[1] Yes \n")
+    print("[0] No \n")
+    file_idx = int(input("Enter selection: \n"))
+    if file_idx == 1:
+        print("Please enter the filepath to the .csv file you would like to analyze. \n")
+        filepath = input("Enter filepath: \n")
+        subject, session = None, None
+    else:  
+        subject = int(input("Enter subject ID#: \n"))
+        session = int(input("Enter session #: \n"))
+        filepath = None
+    
+    eegdevice = analysis_device_prompt()
+    experiment = exp_prompt()
+    
+    return experiment, eegdevice, subject, session, filepath
+
+
 
 def analysis_device_prompt():