pycompound 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

app.py

@@ -25,7 +25,6 @@ import ast
 from numbers import Real
 
 
-
 _LOG_QUEUE: asyncio.Queue[str] = asyncio.Queue()
 
 def _run_with_redirects(fn, writer, *args, **kwargs):
@@ -474,8 +473,15 @@ def run_parameter_tuning_ui(platform: str):
 
 
 
+'''
+app_ui = ui.page_fluid(
+    ui.output_ui("main_ui"),
+    ui.output_text("status_output")
+)
+'''
 
 app_ui = ui.page_fluid(
+    ui.head_content(ui.tags.link(rel="icon", href="emblem.png")),
     ui.output_ui("main_ui"),
     ui.output_text("status_output")
 )
@@ -688,7 +694,6 @@ def server(input, output, session):
         img: ImgData = {"src": str(dir / "www/emblem.png"), "width": "320px", "height": "250px"}
         return img
 
-
     @output
     @render.ui
     def main_ui():
@@ -697,6 +702,7 @@ def server(input, output, session):
                 ui.h2("Main Menu"),
                 ui.div(
                     ui.output_image("image"),
+                    #ui.img(src="emblem.png", width="320px", height="250px"),
                     style=(
                         "position:fixed; top:0; left:50%; transform:translateX(-50%); "
                         "z-index:1000; text-align:center; padding:10px; background-color:white;"
@@ -1122,3 +1128,26 @@ def server(input, output, session):
 app = App(app_ui, server)
 
 
+
+'''
+from starlette.middleware.base import BaseHTTPMiddleware
+from starlette.requests import Request
+
+class _InjectBaseURLMiddleware(BaseHTTPMiddleware):
+    async def dispatch(self, request: Request, call_next):
+        hdrs = dict(request.scope.get("headers", []))
+        if b"rstudio-connect-app-base-url" not in hdrs:
+            host = request.headers.get("x-forwarded-host") or request.headers.get("host") or ""
+            proto = request.headers.get("x-forwarded-proto") or "https"
+            root_path = (request.scope.get("root_path") or "").rstrip("/")
+            base = f"{proto}://{host}{root_path}"
+            new_headers = list(request.scope.get("headers", [])) + [
+                (b"rstudio-connect-app-base-url", base.encode("utf-8"))
+            ]
+            request.scope["headers"] = new_headers
+        return await call_next(request)
+
+app.starlette_app.add_middleware(_InjectBaseURLMiddleware)
+'''
+
+

pycompound/spec_lib_matching.py

@@ -37,6 +37,7 @@ def _eval_one_HRMS(df_query, df_reference, unique_query_ids, unique_reference_id
         LET_threshold=LET_threshold_tmp,
         entropy_dimension=entropy_dimension_tmp,
         high_quality_reference_library=high_quality_reference_library_tmp,
+        verbose=True
     )
 
     return (
@@ -441,21 +442,25 @@ def tune_params_on_NRMS_data_shiny(query_data=None, reference_data=None, grid=No
 
 
 
-def get_acc_HRMS(df_query, df_reference, unique_query_ids, unique_reference_ids, similarity_measure, weights, spectrum_preprocessing_order, mz_min, mz_max, int_min, int_max, window_size_centroiding, window_size_matching, noise_threshold, wf_mz, wf_int, LET_threshold, entropy_dimension, high_quality_reference_library):
+def get_acc_HRMS(df_query, df_reference, unique_query_ids, unique_reference_ids, similarity_measure, weights, spectrum_preprocessing_order, mz_min, mz_max, int_min, int_max, window_size_centroiding, window_size_matching, noise_threshold, wf_mz, wf_int, LET_threshold, entropy_dimension, high_quality_reference_library, verbose=True):
 
     n_top_matches_to_save = 1
 
     all_similarity_scores =  []
     for query_idx in range(0,len(unique_query_ids)):
-        print(f'query spectrum #{query_idx} is being identified')
+        if verbose is True:
+            print(f'query spectrum #{query_idx} is being identified')
         q_idxs_tmp = np.where(df_query.iloc[:,0] == unique_query_ids[query_idx])[0]
         q_spec_tmp = np.asarray(pd.concat([df_query.iloc[q_idxs_tmp,1], df_query.iloc[q_idxs_tmp,2]], axis=1).reset_index(drop=True))
+        #q_spec_tmp = q_spec_tmp.astype(float)
 
         similarity_scores = []
         for ref_idx in range(0,len(unique_reference_ids)):
             q_spec = q_spec_tmp
             r_idxs_tmp = np.where(df_reference.iloc[:,0] == unique_reference_ids[ref_idx])[0]
             r_spec = np.asarray(pd.concat([df_reference.iloc[r_idxs_tmp,1], df_reference.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
+            #print(r_spec)
+            #r_spec = r_spec.astype(float)
 
             is_matched = False
             for transformation in spectrum_preprocessing_order:
@@ -529,7 +534,7 @@ def get_acc_HRMS(df_query, df_reference, unique_query_ids, unique_reference_ids,
 
 
 
-def get_acc_NRMS(df_query, df_reference, unique_query_ids, unique_reference_ids, similarity_measure, weights, spectrum_preprocessing_order, mz_min, mz_max, int_min, int_max, noise_threshold, wf_mz, wf_int, LET_threshold, entropy_dimension, high_quality_reference_library):
+def get_acc_NRMS(df_query, df_reference, unique_query_ids, unique_reference_ids, similarity_measure, weights, spectrum_preprocessing_order, mz_min, mz_max, int_min, int_max, noise_threshold, wf_mz, wf_int, LET_threshold, entropy_dimension, high_quality_reference_library, verbose=True):
 
     n_top_matches_to_save = 1
 
@@ -546,7 +551,7 @@ def get_acc_NRMS(df_query, df_reference, unique_query_ids, unique_reference_ids,
         similarity_scores = []
         for ref_idx in range(0,len(unique_reference_ids)):
             q_spec = q_spec_tmp
-            if ref_idx % 1000 == 0:
+            if verbose is True and ref_idx % 1000 == 0:
                 print(f'Query spectrum #{query_idx} has had its similarity with {ref_idx} reference library spectra computed')
             r_idxs_tmp = np.where(df_reference.iloc[:,0] == unique_reference_ids[ref_idx])[0]
             r_spec_tmp = np.asarray(pd.concat([df_reference.iloc[r_idxs_tmp,1], df_reference.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
@@ -615,7 +620,7 @@ def get_acc_NRMS(df_query, df_reference, unique_query_ids, unique_reference_ids,
 
 
 
-def run_spec_lib_matching_on_HRMS_data(query_data=None, reference_data=None, likely_reference_ids=None, similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, spectrum_preprocessing_order='FCNMWL', high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, window_size_centroiding=0.5, window_size_matching=0.5, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, n_top_matches_to_save=1, print_id_results=False, output_identification=None, output_similarity_scores=None, return_ID_output=False):
+def run_spec_lib_matching_on_HRMS_data(query_data=None, reference_data=None, likely_reference_ids=None, similarity_measure='cosine', weights={'Cosine':0.25,'Shannon':0.25,'Renyi':0.25,'Tsallis':0.25}, spectrum_preprocessing_order='FCNMWL', high_quality_reference_library=False, mz_min=0, mz_max=9999999, int_min=0, int_max=9999999, window_size_centroiding=0.5, window_size_matching=0.5, noise_threshold=0.0, wf_mz=0.0, wf_intensity=1.0, LET_threshold=0.0, entropy_dimension=1.1, n_top_matches_to_save=1, print_id_results=False, output_identification=None, output_similarity_scores=None, return_ID_output=False, verbose=True):
     '''
     runs spectral library matching on high-resolution mass spectrometry (HRMS) data
 
@@ -762,14 +767,13 @@ def run_spec_lib_matching_on_HRMS_data(query_data=None, reference_data=None, lik
 
     all_similarity_scores =  []
     for query_idx in range(0,len(unique_query_ids)):
-        print(f'query spectrum #{query_idx} is being identified')
+        if verbose is True:
+            print(f'query spectrum #{query_idx} is being identified')
         q_idxs_tmp = np.where(df_query.iloc[:,0] == unique_query_ids[query_idx])[0]
         q_spec_tmp = np.asarray(pd.concat([df_query.iloc[q_idxs_tmp,1], df_query.iloc[q_idxs_tmp,2]], axis=1).reset_index(drop=True))
 
         similarity_scores = []
         for ref_idx in range(0,len(unique_reference_ids)):
-            #if ref_idx % 100 == 0:
-            #    print(f'Query spectrum #{query_idx} has had its similarity with {ref_idx} reference library spectra computed')
             q_spec = q_spec_tmp
             r_idxs_tmp = np.where(df_reference.iloc[:,0] == unique_reference_ids[ref_idx])[0]
             r_spec = np.asarray(pd.concat([df_reference.iloc[r_idxs_tmp,1], df_reference.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
@@ -1008,9 +1012,9 @@ def run_spec_lib_matching_on_NRMS_data(query_data=None, reference_data=None, lik
 
         similarity_scores = []
         for ref_idx in range(0,len(unique_reference_ids)):
-            q_spec = q_spec_tmp
-            if ref_idx % 1000 == 0:
+            if verbose is True and ref_idx % 1000 == 0:
                 print(f'Query spectrum #{query_idx} has had its similarity with {ref_idx} reference library spectra computed')
+            q_spec = q_spec_tmp
             r_idxs_tmp = np.where(df_reference.iloc[:,0] == unique_reference_ids[ref_idx])[0]
             r_spec_tmp = np.asarray(pd.concat([df_reference.iloc[r_idxs_tmp,1], df_reference.iloc[r_idxs_tmp,2]], axis=1).reset_index(drop=True))
             r_spec = convert_spec(r_spec_tmp,mzs)

pycompound/tuning_CLI_DE.py

@@ -0,0 +1,233 @@
+
+#!/usr/bin/env python3
+import argparse
+import sys
+import json
+from pathlib import Path
+from typing import Dict, List, Tuple
+import numpy as np
+import pandas as pd
+from scipy.optimize import differential_evolution
+from pycompound.spec_lib_matching import get_acc_HRMS, get_acc_NRMS
+
+
+ALL_PARAMS = [
+    "window_size_centroiding",
+    "window_size_matching",
+    "noise_threshold",
+    "wf_mz",
+    "wf_int",
+    "LET_threshold",
+    "entropy_dimension"
+]
+
+SUGGESTED_BOUNDS = {
+    "window_size_centroiding": (0.0, 0.5),
+    "window_size_matching":    (0.0, 0.5),
+    "noise_threshold":         (0.0, 0.25),
+    "wf_mz":                   (0.0, 5.0),
+    "wf_int":                  (0.0, 5.0),
+    "LET_threshold":           (0.0, 5.0),
+    "entropy_dimension":       (1.0, 3.0)
+}
+
+DEFAULT_PARAMS = {
+    "window_size_centroiding": 0.5,
+    "window_size_matching":    0.5,
+    "noise_threshold":         0.10,
+    "wf_mz":                   0.0,
+    "wf_int":                  1.0,
+    "LET_threshold":           0.0,
+    "entropy_dimension":       1.1
+}
+
+
+# ---------- Utilities ----------
+def parse_bound(s: str) -> Tuple[str, Tuple[float, float]]:
+    # "name=min:max" → (name, (min, max))
+    if "=" not in s or ":" not in s:
+        raise argparse.ArgumentTypeError(f"Bad --bound format '{s}'. Use name=min:max")
+    name, rng = s.split("=", 1)
+    lo, hi = rng.split(":", 1)
+    try:
+        lo_f, hi_f = float(lo), float(hi)
+    except ValueError as e:
+        raise argparse.ArgumentTypeError(f"Non-numeric bound in '{s}': {e}")
+    if lo_f > hi_f:
+        raise argparse.ArgumentTypeError(f"Lower bound > upper bound in '{s}'")
+    return name.strip(), (lo_f, hi_f)
+
+
+def parse_default(s: str) -> Tuple[str, float]:
+    # "name=value" → (name, value)
+    if "=" not in s:
+        raise argparse.ArgumentTypeError(f"Bad --default format '{s}'. Use name=value")
+    name, val = s.split("=", 1)
+    try:
+        v = float(val)
+    except ValueError as e:
+        raise argparse.ArgumentTypeError(f"Non-numeric default in '{s}': {e}")
+    return name.strip(), v
+
+
+def _vector_to_full_params(X: np.ndarray, default_params: Dict[str, float], optimize_params: List[str]) -> Dict[str, float]:
+    params = dict(default_params)
+    for name, val in zip(optimize_params, X):
+        params[name] = float(val)
+    return params
+
+
+# ---------- Objective wrappers (top-level, pickle-friendly) ----------
+def objective_HRMS(X: np.ndarray, ctx: dict) -> float:
+    p = _vector_to_full_params(X, ctx["default_params"], ctx["optimize_params"])
+    acc = get_acc_HRMS(
+        ctx["df_query"], ctx["df_reference"],
+        ctx["uq"], ctx["ur"],
+        ctx["similarity_measure"], ctx["weights"], ctx["spectrum_preprocessing_order"],
+        ctx["mz_min"], ctx["mz_max"], ctx["int_min"], ctx["int_max"],
+        p["window_size_centroiding"], p["window_size_matching"], p["noise_threshold"],
+        p["wf_mz"], p["wf_int"], p["LET_threshold"],
+        p["entropy_dimension"],
+        ctx["high_quality_reference_library"],
+        verbose=False
+    )
+    print(f"\n{ctx['optimize_params']} = {np.array(X)}\naccuracy: {acc*100}%")
+    return 1.0 - acc
+
+
+def objective_NRMS(X: np.ndarray, ctx: dict) -> float:
+    p = _vector_to_full_params(X, ctx["default_params"], ctx["optimize_params"])
+    acc = get_acc_NRMS(
+        ctx["df_query"], ctx["df_reference"],
+        ctx["uq"], ctx["ur"],
+        ctx["similarity_measure"], ctx["weights"], ctx["spectrum_preprocessing_order"],
+        ctx["mz_min"], ctx["mz_max"], ctx["int_min"], ctx["int_max"],
+        p["noise_threshold"], p["wf_mz"], p["wf_int"], p["LET_threshold"], p["entropy_dimension"],
+        ctx["high_quality_reference_library"],
+        verbose=False
+    )
+    print(f"\n{ctx['optimize_params']} = {np.array(X)}\naccuracy: {acc*100}%")
+    return 1.0 - acc
+
+
+# ---------- Main CLI ----------
+def main():
+    p = argparse.ArgumentParser(
+        description="Parameter tuning via Differential Evolution for HRMS/NRMS using pycompound."
+    )
+    p.add_argument("--chromatography_platform", choices=["HRMS", "NRMS"], default="HRMS", help="Chromatography Platform.")
+    p.add_argument("--query_data", required=True, help="Path to query CSV (must contain 'id' column).")
+    p.add_argument("--reference_data", required=True, nargs="+", help="Path(s) to reference CSV(s) (must contain 'id').")
+    p.add_argument("--similarity_measure", default="cosine", choices=["cosine", "renyi", "tsallis"], help="Similarity measure.")
+    p.add_argument("--weights", default="", help="Weights spec; empty means None.")
+    p.add_argument("--spectrum-order", default="CNMWL", help="Spectrum preprocessing order string.")
+    p.add_argument("--mz-min", type=float, default=0.0)
+    p.add_argument("--mz-max", type=float, default=999_999_999.0)
+    p.add_argument("--int-min", type=float, default=0.0)
+    p.add_argument("--int-max", type=float, default=999_999_999.0)
+    p.add_argument("--hq-ref-lib", action="store_true", help="Use high-quality reference library flag.")
+    p.add_argument("--opt", nargs="+", default=["window_size_centroiding", "noise_threshold", "wf_mz", "wf_int"],
+                   help=f"Parameters to optimize (subset of {ALL_PARAMS}).")
+    p.add_argument("--bound", action="append", default=[], type=parse_bound,
+                   help="Bound spec 'name=min:max'. Repeatable.")
+    p.add_argument("--default", dest="defaults", action="append", default=[], type=parse_default,
+                   help="Override a default 'name=value' for non-optimized params or initial values.")
+    p.add_argument("--maxiter", type=int, default=15)
+    p.add_argument("--seed", type=int, default=1)
+    p.add_argument("--workers", type=int, default=-1, help="Use -1 for all cores; 1 to disable parallelism.")
+    args = p.parse_args()
+
+    unknown = [x for x in args.opt if x not in ALL_PARAMS]
+    if unknown:
+        sys.exit(f"Error: unknown --opt params: {unknown}")
+
+    qpath = Path(args.query_data)
+    if not qpath.exists():
+        sys.exit(f"Query CSV not found: {qpath}")
+
+    df_query = pd.read_csv(qpath)
+    if "id" not in df_query.columns:
+        sys.exit("Query CSV must contain an 'id' column.")
+
+    ref_paths = [Path(pth) for pth in args.reference_data]
+    for r in ref_paths:
+        if not r.exists():
+            sys.exit(f"Reference CSV not found: {r}")
+    df_reference = pd.concat([pd.read_csv(r) for r in ref_paths], axis=0, ignore_index=True)
+    if "id" not in df_reference.columns:
+        sys.exit("Reference CSV must contain an 'id' column.")
+
+    uq = df_query["id"].unique().tolist()
+    ur = df_reference["id"].unique().tolist()
+
+    default_params = dict(DEFAULT_PARAMS)
+    for name, val in args.defaults:
+        if name not in DEFAULT_PARAMS:
+            sys.exit(f"--default refers to unknown parameter '{name}'. Allowed: {list(DEFAULT_PARAMS)}")
+        default_params[name] = val
+
+    param_bounds: Dict[str, Tuple[float, float]] = dict(SUGGESTED_BOUNDS)
+    for name, (lo, hi) in args.bound:
+        if name not in SUGGESTED_BOUNDS:
+            sys.exit(f"--bound refers to unknown parameter '{name}'. Allowed: {list(SUGGESTED_BOUNDS)}")
+        param_bounds[name] = (lo, hi)
+
+    bounds = [param_bounds[p] for p in args.opt]
+
+    ctx = dict(
+        df_query=df_query,
+        df_reference=df_reference,
+        uq=uq,
+        ur=ur,
+        similarity_measure=args.similarity_measure,
+        weights=(None if args.weights.strip() == "" else args.weights),
+        spectrum_preprocessing_order=args.spectrum_order,
+        mz_min=float(args.mz_min),
+        mz_max=float(args.mz_max),
+        int_min=float(args.int_min),
+        int_max=float(args.int_max),
+        high_quality_reference_library=bool(args.hq_ref_lib),
+        default_params=default_params,
+        optimize_params=args.opt,
+    )
+
+    history_acc: List[float] = []
+
+    def _cb(xk, convergence):
+        if args.chromatography_platform == "HRMS":
+            acc_pct = (1.0 - objective_HRMS(xk, ctx)) * 100.0
+        else:
+            acc_pct = (1.0 - objective_NRMS(xk, ctx)) * 100.0
+        history_acc.append(acc_pct)
+
+    objective = objective_HRMS if args.chromatography_platform == "HRMS" else objective_NRMS
+
+    result = differential_evolution(
+        objective,
+        bounds=bounds,
+        args=(ctx,),
+        maxiter=int(args.maxiter),
+        tol=0.0,
+        seed=int(args.seed),
+        workers=int(args.workers),
+        callback=_cb,
+    )
+
+    best_params = _vector_to_full_params(result.x, default_params, args.opt)
+    best_acc_pct = (1.0 - result.fun) * 100.0
+
+    print("\n=== Differential Evolution Result ===")
+    print(f"Mode: {args.chromatography_platform}")
+    print(f"Optimized over: {args.opt}")
+    print("Best values (selected params):")
+    for name in args.opt:
+        print(f"  {name}: {best_params[name]}")
+    print("\nFull parameter set used in final evaluation:")
+    for k in ALL_PARAMS:
+        print(f"  {k}: {best_params[k]}")
+    print(f"\nBest accuracy: {best_acc_pct:.3f}%")
+    print(f"DE raw: success={result.success}, nfev={result.nfev}, nit={result.nit}, message='{result.message}'")
+
+if __name__ == "__main__":
+    main()
+

pycompound/{tuning_CLI.py → tuning_CLI_grid.py}

@@ -1,6 +1,6 @@
 
-from pycompound.spec_lib_matching import tune_params_on_HRMS_data
-from pycompound.spec_lib_matching import tune_params_on_NRMS_data
+from pycompound.spec_lib_matching import tune_params_on_HRMS_data_grid
+from pycompound.spec_lib_matching import tune_params_on_NRMS_data_grid
 import argparse
 import json
 from pathlib import Path
@@ -61,9 +61,9 @@ grid['entropy_dimension'] = [float(x) for x in grid['entropy_dimension']]
 
 
 if args.chromatography_platform == 'HRMS':
-    tune_params_on_HRMS_data(query_data=args.query_data, reference_data=args.reference_data, grid=grid, output_path=args.output_path)
+    tune_params_on_HRMS_data_grid(query_data=args.query_data, reference_data=args.reference_data, grid=grid, output_path=args.output_path)
 
 if args.chromatography_platform == 'NRMS':
-    tune_params_on_NRMS_data(query_data=args.query_data, reference_data=args.reference_data, grid=grid, output_path=args.output_path)
+    tune_params_on_NRMS_data_grid(query_data=args.query_data, reference_data=args.reference_data, grid=grid, output_path=args.output_path)
 
 

{pycompound-0.1.3.dist-info → pycompound-0.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycompound
-Version: 0.1.3
+Version: 0.1.4
 Summary: Python package to perform compound identification in mass spectrometry via spectral library matching.
 Author-email: Hunter Dlugas <fy7392@wayne.edu>
 License-Expression: MIT

pycompound-0.1.4.dist-info/RECORD

@@ -0,0 +1,15 @@
+app.py,sha256=e_QULBLubrZLk_huIyDvL64lFzgDRo_vaYV0MIx9VJQ,51950
+pycompound/build_library.py,sha256=sXG5MTJnPE7Gr8YMlLWjfMS7JQrW32lCeCGDw-DFe38,4826
+pycompound/plot_spectra.py,sha256=_yeHooNoJHYlTajaZ9hgUudisdWVlw1Zw1wJfV3tpqc,40632
+pycompound/plot_spectra_CLI.py,sha256=ObaLad5Z5DmfQB-j0HSCg1mLORbYj2BM3hb5Yd0ZdDI,8395
+pycompound/processing.py,sha256=q629rcDaMQMgef-4SbeV9cJnuiLXg97VT2F5AIsyqgI,10654
+pycompound/similarity_measures.py,sha256=NbeVIy9DE_KWlDMXXylekjKuYVrtzbeEXbTutKFxmfU,10460
+pycompound/spec_lib_matching.py,sha256=TBH7cZLeIWNk5XkXcN7kiBfCSe6eRkseXIPMMLB54iI,67261
+pycompound/spec_lib_matching_CLI.py,sha256=qiekC52FP6ET_3NYvxUDN7km7y1OLUsd9FB4SHfne_Y,9690
+pycompound/tuning_CLI_DE.py,sha256=PXy95LD_jmVeWdgiMlMwEZU_KqPGqDao1skwe5U4Sfc,9147
+pycompound/tuning_CLI_grid.py,sha256=0XU-4ShZiZ2MQy5d0zydH0hphqXvqGtf4etl-ePNarU,8560
+pycompound-0.1.4.dist-info/licenses/LICENSE,sha256=fPFFlkSGg60VQWyWqTSv8yoJnpLzppzdihVWY5NKom8,1064
+pycompound-0.1.4.dist-info/METADATA,sha256=qlCzW19-6MpmuGoHbmQVL9ljKRCO4JXZ55-GTyKc3_I,1732
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