major rework and splitting of files. update documentation

README.md

@@ -2,16 +2,27 @@
 
 This repository contains the back-end of the [Virtual FTIR Spectrometer](https://github.com/RastonLab/Virtual-FTIR-Spectrometer).
 
-## [flask](https://github.com/RastonLab/Virtual-FTIR-Functions/tree/main/flask)
+## [api](https://github.com/RastonLab/Virtual-FTIR-Functions/tree/main/api)
 
-This directory holds the Flask web framework that the front-end reaches out to.
+This directory contains
+
+- `background.py`
+  - Contains a program that strictly generates a background sample. This program uses `data.json` for its input and is capable of graphing using `mathplotlib`.
+- `fast_api.py`
+  - Contains a program that accepts API calls for both a background sample and spectrum. This program accepts JSON through a `fetch()` or `cURL` command and returns JSON of X and Y coordinates.
+- `flask_api`
+  - Contains a program that accepts API calls for both a background sample and spectrum. This program accepts JSON through a `fetch()` or `cURL` command and returns JSON of X and Y coordinates.
+- `functions.py`
+  - Contains functions used in all other files. Designed so edits only need to be made to one file for main functionality updates and changes.
+- `spectrum.py`
+  - Contains a program that strictly generates a spectrum. This program uses `data.json` for its input and is capable of graphing using `mathplotlib`.
 
 ## [jupyter-notebook](https://github.com/RastonLab/Virtual-FTIR-Functions/tree/main/jupyter-notebook)
 
 This directory holds a Jupyter Notebook that was used in the testing and development of the spectrum modification functions. These functions emulate the blackbody spectrum (sPlanck), the beamsplitter, the cell windows, and the detector response spectrum.
 
 ## [create-virtual-environments.sh](https://github.com/RastonLab/Virtual-FTIR-Functions/blob/main/create-virtual-environments.sh)
 
-This script creates a virtual python environments (venv) needed to run the files in the `flask` and `jupyter-notebook` directories. The script uses `requirements.txt` to install the required dependencies to a venv that is used for both directories.
+This script creates a virtual python environments (venv) needed to run the files in the `api` and `jupyter-notebook` directories. The script uses `requirements.txt` to install the required dependencies to a venv that is used for both directories.
 
-To activate the virtual environment (venv), run `source venv/bin/activate` in the terminal. To deactivate the virtual enviornment (venv), run `deactivate` in the terminal.
+To activate the virtual environment (venv), run `source venv/bin/activate` in the terminal. To deactivate the virtual environment (venv), run `deactivate` in the terminal.

flask/README.md → api/README.md

@@ -1,6 +1,6 @@
 # Virtual-FTIR-Functions
 
-## flask
+## api
 
 ### `background.py`
 

flask/background.py → api/background.py

@@ -4,12 +4,10 @@
 
 from functions import __param_check, __generate_background
 
-bool
-
 
 def main():
     # read local data file into a dictionary
-    with open("data.json", "r") as data_json:
+    with open("../data.json", "r") as data_json:
         data = json.load(data_json)
 
     print(data)

api/fast_api.py

@@ -0,0 +1,186 @@
+# FastAPI server
+#   https://fastapi.tiangolo.com/
+#   uvicorn fast_api:app --reload
+
+# https://realpython.com/fastapi-python-web-apis/
+from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware
+from pydantic import BaseModel
+from typing import Literal
+
+from functions import __param_check, __generate_spectra, __generate_background
+
+molecule_list = Literal[
+    "C2H2",
+    "C2H4",
+    "C2H6",
+    "C2N2",
+    "C4H2",
+    "CF4",
+    "CH3Br",
+    "CH3Cl",
+    "CH3CN",
+    "CH3OH",
+    "CH4",
+    "ClO",
+    "ClONO2",
+    "CO",
+    "CO2",
+    "COCl2",
+    "COF2",
+    "CS",
+    "H2",
+    "H2CO",
+    "H2O",
+    "H2O2",
+    "H2S",
+    "HBr",
+    "HC3N",
+    "HCl",
+    "HCN",
+    "HCOOH",
+    "HF",
+    "HI",
+    "HNO3",
+    "HO2",
+    "HOBr",
+    "HOCl",
+    "N2",
+    "N2O",
+    "NH3",
+    "NO",
+    "NO+",
+    "NO2",
+    "O",
+    "O2",
+    "O3",
+    "OCS",
+    "OH",
+    "PH3",
+    "SF6",
+    "SO2",
+    "SO3",
+]
+
+
+class Payload(BaseModel):
+    minWave: float
+    maxWave: float
+    molecule: molecule_list
+    pressure: float
+    resolution: float
+    numScan: int
+    zeroFill: Literal[0, 1, 2]
+    source: Literal[1700, 3100]
+    beamsplitter: Literal["AR_ZnSe", "AR_CaF2"]
+    cellWindow: Literal["ZnSe", "CaF2"]
+    detector: Literal["MCT", "InSb"]
+
+
+app = FastAPI()
+origins = [
+    "http://localhost:3000",
+]
+
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=origins,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+
+@app.get("/")
+async def root():
+    return "<h1>ftir</h1>"
+
+
+@app.post("/fetch_background/")
+async def create_item(payload: Payload):
+    data = {
+        "minWave": payload.minWave,
+        "maxWave": payload.maxWave,
+        "molecule": payload.molecule,
+        "pressure": payload.pressure,
+        "resolution": payload.resolution,
+        "numScan": payload.numScan,
+        "zeroFill": payload.zeroFill,
+        "source": payload.source,
+        "beamsplitter": payload.beamsplitter,
+        "cellWindow": payload.cellWindow,
+        "detector": payload.detector,
+    }
+
+    # verify the information in the dictionary
+    __param_check(data)
+
+    print("----- output verified params to console as self-check -----")
+    for key, value in data.items():
+        print("  %s: %s" % (key, value))
+
+    # perform: transmission spectrum of gas sample (calc_spectrum)
+    #      --> blackbody spectrum of source (sPlanck)
+    #      --> transmission spectrum of beamsplitter and cell windows
+    #      --> detector response spectrum
+    print("----- start __generate_background() -----")
+    result = __generate_background(data)
+    print("----- end __generate_background() -----")
+
+    if result != False:
+        # convert dictionary values to strings and return as JSON
+        return {
+            "success": True,
+            "x": list(result.keys()),
+            "y": [str(flt) for flt in result.values()],
+        }
+    else:
+        return {
+            "success": False,
+            "text": "No line in the specified wavenumber range",
+        }
+
+
+@app.post("/post_json/")
+async def create_item(payload: Payload):
+    data = {
+        "minWave": payload.minWave,
+        "maxWave": payload.maxWave,
+        "molecule": payload.molecule,
+        "pressure": payload.pressure,
+        "resolution": payload.resolution,
+        "numScan": payload.numScan,
+        "zeroFill": payload.zeroFill,
+        "source": payload.source,
+        "beamsplitter": payload.beamsplitter,
+        "cellWindow": payload.cellWindow,
+        "detector": payload.detector,
+    }
+
+    # verify the information in the dictionary
+    __param_check(data)
+
+    print("----- output verified params to console as self-check -----")
+    for key, value in data.items():
+        print("  %s: %s" % (key, value))
+
+    # perform: transmission spectrum of gas sample (calc_spectrum)
+    #      --> blackbody spectrum of source (sPlanck)
+    #      --> transmission spectrum of beamsplitter and cell windows
+    #      --> detector response spectrum
+    print("----- start __generate_spectra() -----")
+    result = __generate_spectra(data)
+    print("----- end __generate_spectra() -----")
+
+    if result != False:
+        # convert dictionary values to strings and return as JSON
+        return {
+            "success": True,
+            "x": list(result.keys()),
+            "y": [str(flt) for flt in result.values()],
+        }
+    else:
+        return {
+            "success": False,
+            "text": "No line in the specified wavenumber range",
+        }

flask/flask.py → api/flask_api.py

@@ -1,3 +1,7 @@
+# Flask server
+#   https://flask.palletsprojects.com/en/2.2.x/
+#   python3 flask_api.py
+
 from flask import Flask, request
 from flask_cors import CORS
 

flask/calculate.py → api/spectrum.py

@@ -7,7 +7,7 @@
 
 def main():
     # read local data file into a dictionary
-    with open("data.json", "r") as data_json:
+    with open("../data.json", "r") as data_json:
         data = json.load(data_json)
 
     print(data)

create-virtual-environments.sh

@@ -10,6 +10,4 @@ source venv/bin/activate
 
 pip install -r requirements.txt
 
-deactivate
-
 echo "------ script finished ------"

download_hitran.py

@@ -0,0 +1,56 @@
+# this script installs the HITRAN data for the following molecules locally
+#   the commented out molecules do not download properly but are included in the UI
+from radis.io.hitran import fetch_hitran
+
+for molecule in [
+    "C2H2",
+    "C2H4",
+    "C2H6",
+    "C2N2",
+    "C4H2",
+    # "CF4",
+    "CH3Br",
+    "CH3Cl",
+    "CH3CN",
+    "CH3OH",
+    "CH4",
+    "ClO",
+    # "ClONO2",
+    "CO",
+    "CO2",
+    "COCl2",
+    "COF2",
+    "CS",
+    "H2",
+    "H2CO",
+    "H2O",
+    "H2O2",
+    "H2S",
+    "HBr",
+    "HC3N",
+    "HCl",
+    "HCN",
+    "HCOOH",
+    "HF",
+    "HI",
+    "HNO3",
+    "HO2",
+    "HOBr",
+    "HOCl",
+    "N2",
+    "N2O",
+    "NH3",
+    "NO",
+    "NO+",
+    "NO2",
+    "O",
+    "O2",
+    "O3",
+    "OCS",
+    "OH",
+    "PH3",
+    # "SF6",
+    "SO2",
+    "SO3",
+]:
+    fetch_hitran(molecule, parse_quanta=molecule in ["CO", "CO2"])

requirements.txt

@@ -5,3 +5,9 @@ specutils
 # used by flask
 flask
 flask-cors
+
+# used by fast
+fastapi
+
+# formatting
+black