added download peaks and other fixes

src/pages/apply_calibration.py

@@ -422,6 +422,7 @@ def load_tabs_target_spectrum():
     x_calib = st.session_state["cache_bools"]["x_calib"]
     y_calib = st.session_state["cache_bools"]["y_calib"]
 
+    print(x_calib, y_calib)
     target_spe = st.session_state["cache_dicts"]["page01_load_spe"][
         "target_spe_current"
     ]
@@ -484,9 +485,9 @@ def load_tabs_target_spectrum():
             file_name="xcalibrated_spectrum.csv",
         )
 
-        spe_target = target_calibrated
+        target_spe = target_calibrated
 
-    if x_calib:
+    if y_calib:
 
         ycalmodel = st.session_state["cache_dicts"]["y_calibration"][
             "ycalibration_model"
@@ -495,12 +496,15 @@ def load_tabs_target_spectrum():
 
         ax = spe_srm.plot(label="SRM experimental", color="red")
 
-        spe_target.plot(ax=ax, label="Target spectrum", color="blue")
+        target_spe.plot(ax=ax, label="Target spectrum", color="blue")
 
-        spe_ycalibrated = ycalmodel.process(spe_target)
+        spe_ycalibrated = ycalmodel.process(target_spe)
 
         spe_ycalibrated.plot(label="Y-calibrated", color="green", ax=ax.twinx())
         fig = ax.get_figure()
+
+        spe_units = target_spe.meta["units"]
+        ax.set_xlabel(r"Raman shift " + spe_units)
         st.pyplot(fig)
 
         csv = io_write_csv(spe_ycalibrated.x, spe_ycalibrated.y)

src/pages/load_instrument_settings.py

@@ -1,18 +1,14 @@
 #!/usr/bin/env python3
-import streamlit_pydantic as sp
-from pydantic import BaseModel, Field, ValidationError, parse_obj_as
-from typing import Set
-from enum import Enum
 from collections import defaultdict
 from copy import deepcopy
+from enum import Enum
 
-import pandas as pd
-
-from typing import TypedDict
+from typing import Set, TypedDict
 
-from pydantic import BaseModel, Field
+import pandas as pd
 
 import streamlit as st
+import streamlit_pydantic as sp
 from front_end.htmlTemplates import css
 
 from modules.navigation_bar import navbar
@@ -25,6 +21,8 @@
     update_session_state,
 )
 
+from pydantic import BaseModel, Field, parse_obj_as, ValidationError
+
 from ramanchada2.protocols.calibration import (
     CalibrationModel,
     CertificatesDict,
@@ -34,8 +32,6 @@
     YCalibrationComponent,
 )
 
-from ramanchada2.protocols.calibration import CalibrationModel
-
 
 # class InstrumentsMandatory(BaseModel):
 #     laser_wavelength: int = 532
@@ -46,23 +42,29 @@
     settings = st.session_state["cache_dicts"]["instrument_settings"]["settings"]
 else:
     settings = defaultdict(str)
-    settings['laser_wavelength'] = 532
+    settings["laser_wavelength"] = 532
 
 
 class InstrumentSettings(BaseModel):
-    make_and_model_of_the_instrument: str | None = settings['make_and_model_of_the_instrument']
-    serial_number_of_the_instrument: str = settings['serial_number_of_the_instrument']
-    laser_wavelength: int = settings['laser_wavelength']
+    make_and_model_of_the_instrument: str | None = settings[
+        "make_and_model_of_the_instrument"
+    ]
+    serial_number_of_the_instrument: str = settings["serial_number_of_the_instrument"]
+    laser_wavelength: int = Field(
+        settings["laser_wavelength"],
+        description="Units: nm",
+        title="Lazer wavelength (nm)",
+    )
     # serial_number: str | None = settings['serial_number']
     # description: str | None = settings['description']
     # Another
     # instrument_model: str | None = settings['instrument_model']
-    device_type: str | None = settings['device_type']
+    device_type: str | None = settings["device_type"]
     # Optical path details
     # laser_waveletgth: str
-    numerical_aperture: str | None = settings['numerical_aperture']
-    grating: str | None = settings['grating']
-    slit: str | None = settings['slit']
+    numerical_aperture: str | None = settings["numerical_aperture"]
+    grating: str | None = settings["grating"]
+    slit: str | None = settings["slit"]
     # pinhole: str | None = settings[]
     # # Acquisition parameters
     # exposure_time: str | None = settings[]
@@ -146,8 +148,7 @@ class InstrumentSettings(BaseModel):
 
 data = sp.pydantic_input(key="my_form", model=InstrumentSettings)
 if data:
-    st.session_state["cache_dicts"]["instrument_settings"]["settings"] = dict(
-        data)
+    st.session_state["cache_dicts"]["instrument_settings"]["settings"] = dict(data)
 # if True:
 #     print('Delete AFTER ')
 #     keys = [k for k in st.session_state.keys() if 'my_form' in k]

src/pages/load_or_create_calibration.py

@@ -881,6 +881,12 @@ def process_x_calibration_neon_creation():
                 axs[1].set_xlabel(xlabel)
                 fig = axs[1].get_figure()
 
+                st.download_button(
+                    "Download Peaks found (JSON)",
+                    data=neon_peak_candidates.json(),
+                    file_name="neon_peaks_found.json",
+                )
+
             if use_peak_find:
                 st.session_state["cache_dicts"]["spectra_x_peak_candidates"][
                     "neon"
@@ -1627,6 +1633,12 @@ def process_x_calibration_si_creation():
                 axs[1].set_xlabel(xlabel)
                 fig = axs[1].get_figure()
 
+                st.download_button(
+                    "Download Peaks found (JSON)",
+                    data=si_peak_candidates.json(),
+                    file_name="si_peaks_found.json",
+                )
+
             if use_peak_find:
                 st.session_state["cache_dicts"]["spectra_x_peak_candidates"][
                     "si"