ararpy 0.0.1a1__py3-none-any.whl

ararpy/calc/spectra.py

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+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2023 Yang
+# ararpy - calc- spectra
+# ==========================================
+#
+# Spectra
+#
+"""
+import numpy as np
+
+
+def get_data(y: list, sy: list, x: list, f: int = 1, indices: list = None,
+             cumulative: bool = False, successive: bool = True):
+    """
+    Get spectra data based on passed x, y, and sy.
+
+    Parameters
+    ----------
+    y :
+    sy :
+    x :
+    f : error factor of sy, 1 or 2 for 1 or 2 sigma
+    indices : array-like, default None for all sequences included
+        An array of ints indicating which sequences to include.
+    cumulative : bool, default False.
+        This parameter should be True if x is already cumulative.
+    successive : If setting indices successive
+
+    Returns
+    -------
+    list of lists of float. [x, y1, y2]
+    """
+    if np.issubdtype(type(f), np.integer) and f > 1:
+        sy = np.divide(sy, f)
+    dp = np.shape([y, sy, x])[-1]
+    if indices is None:
+        indices = list(range(dp))
+    if successive:
+        indices = list(range(min(indices), max(indices) + 1))
+    if not cumulative:
+        x = np.divide(np.cumsum(x) * 100, sum(x)).tolist()
+    k0, k1, k2 = [], [], []
+    for i in range(dp):
+        if i not in indices:
+            continue
+        else:
+            k0.append([x[i - 1], 0][i == 0])
+            k0.append(x[i])
+            k1.append(y[i] + sy[i] if i % 2 == 0 else y[i] - sy[i])
+            k1.append(y[i] + sy[i] if i % 2 == 0 else y[i] - sy[i])
+            k2.append(y[i] - sy[i] if i % 2 == 0 else y[i] + sy[i])
+            k2.append(y[i] - sy[i] if i % 2 == 0 else y[i] + sy[i])
+    # Close the spectrum
+    k0.insert(0, k0[0])
+    k0.append(k0[-1])
+    k1.insert(0, k2[0])
+    k1.append(k2[-1])
+    k2.insert(0, k1[0])
+    k2.append(k1[-1])
+    return [k0, k1, k2]

ararpy/files/__init__.py

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+from . import calc_file, arr_file, raw_file, new_file, json, basic, raw, xls, export
+

ararpy/files/arr_file.py

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+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2023 Yang
+# ararpy - files - arr_file
+# ==========================================
+#
+#
+#
+"""
+# === External imports ===
+import os
+import pickle
+
+from .. import smp
+
+SAMPLE_MODULE = smp.Sample().__module__
+
+
+def to_sample(file_path, sample_name: str = ""):
+    """
+    file_path: full path of input file
+    name： samplename
+    return sample instance
+    """
+    try:
+        with open(file_path, 'rb') as f:
+            sample = renamed_load(f)
+    except (Exception, BaseException):
+        raise ValueError(f"Fail to open arr file: {file_path}")
+    # Check arr version
+    # recalculation will not be applied automatically
+    sample = check_version(sample)
+    return sample
+
+
+def save(file_path, sample: smp.Sample):
+    """ Save arr project as arr files
+
+    Parameters
+    ----------
+    file_path : str, filepath
+    sample : Sample instance
+
+    Returns
+    -------
+    str, file name
+    """
+    file_path = os.path.join(file_path, f"{sample.Info.sample.name}.arr")
+    with open(file_path, 'wb') as f:
+        f.write(pickle.dumps(sample))
+    # with open(file_path, 'w') as f:
+    # # save serialized json data to a readable text
+    #     f.write(basic_funcs.getJsonDumps(sample))
+    return f"{sample.Info.sample.name}.arr"
+
+
+def check_version(sample: smp.Sample):
+    """
+
+    Parameters
+    ----------
+    sample
+
+    Returns
+    -------
+
+    """
+    if sample.version != smp.VERSION:
+        smp.initial.re_set_smp(sample)
+    return sample
+
+
+class RenameUnpickler(pickle.Unpickler):
+    def find_class(self, module: str, name: str):
+        renamed_module = module
+        if '.sample' in module and module != SAMPLE_MODULE:
+            renamed_module = SAMPLE_MODULE
+
+        return super(RenameUnpickler, self).find_class(renamed_module, name)
+
+
+def renamed_load(file_obj):
+    return RenameUnpickler(file_obj).load()
+

ararpy/files/basic.py

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+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2023 Yang
+# ararpy - files - basic
+# ==========================================
+#
+#
+#
+"""
+# from programs.ararpy.files import json as myjson
+from ..files import json as myjson
+
+import os
+import pickle
+import traceback
+import json
+
+
+try:
+    from webarar.settings import SETTINGS_ROOT
+except ModuleNotFoundError:
+    SETTINGS_ROOT = ""
+
+
+def upload(file, media_dir):
+    try:
+        name, suffix = os.path.splitext(file.name)
+        if suffix not in [
+            '.xls', '.age', '.xlsx', '.arr', '.jpg', '.png', '.txt',
+            '.log', '.seq', '.json', '.ahd']:
+            raise TypeError("Wrong File")
+        web_file_path = os.path.join(media_dir, file.name)
+        with open(web_file_path, 'wb') as f:
+            for chunk in file.chunks():
+                f.write(chunk)
+        print("File path on the server: %s" % web_file_path)
+    except PermissionError:
+        raise ValueError(f'Permission denied')
+    except (Exception, BaseException) as e:
+        print(traceback.format_exc())
+        raise ValueError(f'Error in opening file: {e}')
+    else:
+        return web_file_path, name, suffix
+
+
+def read(file_path):
+    """ Read text files, default 'r', 'rb'
+    Parameters
+    ----------
+    file_path
+
+    Returns
+    -------
+
+    """
+    try:
+        with open(file_path, 'r') as f:
+            params = json.load(f)
+    except UnicodeDecodeError:
+        with open(file_path, 'rb') as f:
+            params = pickle.load(f)
+    return params
+
+
+def write(file_path, params):
+    """
+    Parameters
+    ----------
+    file_path
+    params
+
+    Returns
+    -------
+
+    """
+    # with open(file_path, 'wb') as f:
+    #     f.write(pickle.dumps(params))
+    with open(file_path, 'w') as f:  # save serialized json data to a readable text
+        f.write(myjson.dumps(params))
+    return file_path
+
+
+def delete(file_path):
+    """
+    Parameters
+    ----------
+    file_path
+
+    Returns
+    -------
+
+    """
+    try:
+        os.remove(file_path)
+    except Exception:
+        return False
+    else:
+        return True