Added multi-thresh simulation to "full" and "short" (currently running).

Added complete "rect-lp" analysis except figure.
Added multiple appendix figs.
Overhauled normalization options across all condense scripts.

Co-authored-by: Copilot <copilot@github.com>

python/collect_inv_data_rect-lp.py

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+import numpy as np
+from thunderhopper.filetools import search_files
+from thunderhopper.modeltools import load_data, save_data
+from IPython import embed
+
+# GENERAL SETTINGS:
+mode = ['pure', 'noise'][1]
+target_species = [
+    'Chorthippus_biguttulus',
+    'Chorthippus_mollis',
+    'Chrysochraon_dispar',
+    'Euchorthippus_declivus',
+    'Gomphocerippus_rufus',
+    'Omocestus_rufipes',
+    'Pseudochorthippus_parallelus',
+]
+stages = ['filt', 'env']
+search_path = '../data/inv/rect_lp/'
+save_path = '../data/inv/rect_lp/collected/'
+
+# EXECUTION:
+for i, species in enumerate(target_species):
+    print(f'Processing {species}')
+
+    # Fetch all species-specific song files:
+    all_paths = search_files(species, incl=mode, ext='npz', dir=search_path)
+    
+    # Run through files:
+    for j, path in enumerate(all_paths):
+
+        # Load invariance data:
+        data, config = load_data(path, 'scales', 'measure')
+
+        if j == 0:
+            # Prepare species-specific storage:
+            species_data = dict(scales=data['scales'])
+            for stage in stages:
+                mkey = f'measure_{stage}'
+                shape = data[mkey].shape + (len(all_paths),)
+                species_data[mkey] = np.zeros(shape, dtype=float)
+        
+        # Log species data:
+        for stage in stages:
+            mkey = f'measure_{stage}'
+            species_data[mkey][..., j] = data[mkey]
+
+    # Save collected file data:
+    save_name = save_path + species + '_' + mode
+    save_data(save_name, species_data, config, overwrite=True)
+
+print('Done.')