pychemstation 0.10.7__py3-none-any.whl → 0.10.8.dev1__py3-none-any.whl

pychemstation/utils/spec_utils.py

@@ -3,23 +3,22 @@ Module contains various utility function for spectral data processing and
 analysis.
 """
 
+from typing import Optional
+
 import numpy as np
 import scipy
 
 from ..utils.num_utils import find_nearest_value_index
 
 
-def create_binary_peak_map(data):
+def create_binary_peak_map(data: np.ndarray) -> np.ndarray:
     """Return binary map of the peaks within data points.
 
     True values are assigned to potential peak points, False - to baseline.
 
-    Args:
-        data (:obj:np.array): 1D array with data points.
+    :param data: 1D array with data points.
 
-    Returns:
-        :obj:np.array, dtype=bool: Mapping of data points, where True is
-            potential peak region point, False - baseline.
+    :return: Mapping of data points, where True is potential peak region point, False - baseline.
     """
     # copying array
     data_c = np.copy(data)
@@ -47,21 +46,15 @@ def create_binary_peak_map(data):
     return peak_map
 
 
-def combine_map_to_regions(mapping):
+def combine_map_to_regions(mapping: np.ndarray) -> np.ndarray:
     """Combine True values into their indexes arrays.
 
-    Args:
-        mapping (:obj:np.array): Boolean mapping array to extract the indexes
-            from.
-
-    Returns:
-        :obj:np.array: 2D array with left and right borders of regions, where
-            mapping is True.
+    :param mapping: Boolean mapping array to extract the indexes from.
+    :return: 2D array with left and right borders of regions, where mapping is True.
 
     Example:
-        >>> combine_map_to_regions(np.array([True, True, False, True, False]))
-        array([[0, 1],
-                [3, 3]])
+    >>> combine_map_to_regions(np.array([True, True, False, True, False]))
+    ...     array([[0, 1], [3, 3]])
     """
 
     # No peaks identified, i.e. mapping is all False
@@ -94,23 +87,17 @@ def combine_map_to_regions(mapping):
     return np.hstack((lefts, rights))
 
 
-def filter_regions(x_data, peaks_regions):
+def filter_regions(x_data: np.ndarray, peaks_regions: np.ndarray) -> np.ndarray:
     """Filter peak regions.
 
     Peak regions are filtered to remove potential false positives (e.g. noise
         spikes).
 
-    Args:
-        x_data (:obj:np.array): X data points, needed to pick up the data
-            resolution and map the region indexes to the corresponding data
+    :param x_data: X data points, needed to pick up the data resolution and map the region indexes to the corresponding data
             points.
-        y_data (:obj:np.array): Y data points, needed to validate if the peaks
-            are actually present in the region and remove invalid regions.
-        peaks_regions (:obj:np.array): 2D Nx2 array with peak regions indexes
-            (rows) as left and right borders (columns).
+    :param peaks_regions: 2D Nx2 array with peak regions indexes (rows) as left and right borders (columns).
 
-    Returns:
-        :obj:np.array: 2D Mx2 array with filtered peak regions indexes(rows) as
+    :return: 2D Mx2 array with filtered peak regions indexes(rows) as
             left and right borders (columns).
     """
 
@@ -134,21 +121,19 @@ def filter_regions(x_data, peaks_regions):
     return peaks_regions
 
 
-def filter_noisy_regions(y_data, peaks_regions):
+def filter_noisy_regions(y_data: np.ndarray, peaks_regions: np.ndarray) -> np.ndarray:
     """Remove noisy regions from given regions array.
 
     Peak regions are filtered to remove false positive noise regions, e.g.
         incorrectly assigned due to curvy baseline. Filtering is performed by
         computing average peak points/data points ratio.
 
-    Args:
-        y_data (:obj:np.array): Y data points, needed to validate if the peaks
+    :param y_data: Y data points, needed to validate if the peaks
             are actually present in the region and remove invalid regions.
-        peaks_regions (:obj:np.array): 2D Nx2 array with peak regions indexes
+    :param peaks_regions: 2D Nx2 array with peak regions indexes
             (rows) as left and right borders (columns).
 
-    Returns:
-        :obj:np.array: 2D Mx2 array with filtered peak regions indexes(rows) as
+    :return: 2D Mx2 array with filtered peak regions indexes(rows) as
             left and right borders (columns).
     """
 
@@ -198,42 +183,35 @@ def filter_noisy_regions(y_data, peaks_regions):
     return peaks_regions
 
 
-def merge_regions(x_data, peaks_regions, d_merge, recursively=True):
+def merge_regions(
+    x_data: np.ndarray,
+    peaks_regions: np.ndarray,
+    d_merge: float,
+    recursively: Optional[bool] = True,
+):
     """Merge peak regions if distance between is less than delta.
 
-    Args:
-        x_data (:obj:np.array): X data points.
-        peaks_regions (:obj:np.array): 2D Nx2 array with peak regions indexes
+    :param x_data: X data points.
+    :param peaks_regions: 2D Nx2 array with peak regions indexes
             (rows) as left and right borders (columns).
-        d_merge (float): Minimum distance in X data points to merge two or more
+    :param d_merge: Minimum distance in X data points to merge two or more
             regions together.
-        recursively (bool, optional): If True - will repeat the procedure until
+    :param recursively: If True - will repeat the procedure until
             all regions with distance < than d_merge will merge.
 
-    Returns:
-        :obj:np.array: 2D Mx2 array with peak regions indexes (rows) as left and
+    :return: 2D Mx2 array with peak regions indexes (rows) as left and
             right borders (columns), merged according to predefined minimal
             distance.
 
     Example:
-        >>> regions = np.array([
-                [1, 10],
-                [11, 20],
-                [25, 45],
-                [50, 75],
-                [100, 120],
-                [122, 134]
-            ])
-        >>> data = np.ones_like(regions) # ones as example
-        >>> merge_regions(data, regions, 1)
-        array([[  1,  20],
-               [ 25,  45],
-               [ 50,  75],
-               [100, 120],
-               [122, 134]])
-        >>> merge_regions(data, regions, 20, True)
-        array([[  1,  75],
-               [100, 134]])
+    >>> regions = np.array(
+    ...     [[1, 10], [11, 20], [25, 45], [50, 75], [100, 120], [122, 134]]
+    ... )
+    >>> data = np.ones_like(regions)  # ones as example
+    >>> merge_regions(data, regions, 1)
+    ...     array([[1, 20],  [ 25,  45],  [ 50,  75],  [100, 120],  [122, 134]])
+    >>> merge_regions(data, regions, 20, True)
+    ...     array([[1, 75], [100, 134]])
     """
     # the code is pretty ugly but works
     merged_regions = []
@@ -269,17 +247,15 @@ def merge_regions(x_data, peaks_regions, d_merge, recursively=True):
     return merge_regions(x_data, merged_regions, d_merge, recursively=True)
 
 
-def expand_regions(x_data, peaks_regions, d_expand):
+def expand_regions(x_data: np.ndarray, peaks_regions: np.ndarray, d_expand: float):
     """Expand the peak regions by the desired value.
 
-    Args:
-        x_data (:obj:np.array): X data points.
-        peaks_regions (:obj:np.array): 2D Nx2 array with peak regions indexes
+    :param x_data: X data points.
+    :param peaks_regions: 2D Nx2 array with peak regions indexes
             (rows) as left and right borders (columns).
-        d_expand (float): Value to expand borders to (in X data scale).
+    :param d_expand: Value to expand borders to (in X data scale).
 
-    Returns:
-        :obj:np.array: 2D Nx2 array with expanded peak regions indexes (rows) as
+    :return: 2D Nx2 array with expanded peak regions indexes (rows) as
             left and right borders (columns).
     """
 

pychemstation/utils/table_types.py

@@ -6,6 +6,10 @@ from typing import TypeVar
 
 
 class TableOperation(Enum):
+    """
+    MACROS related to editing and reading tables in Chemstation.
+    """
+
     def __str__(self):
         return "%s" % self.value
 
@@ -29,6 +33,10 @@ class TableOperation(Enum):
 
 
 class RegisterFlag(Enum):
+    """
+    Flags for accessing Chemstation parameters.
+    """
+
     def __str__(self):
         return "%s" % self.value
 
@@ -42,7 +50,7 @@ class RegisterFlag(Enum):
     SOLVENT_D_COMPOSITION = "PumpChannel4_CompositionPercentage"
     FLOW = "Flow"
     MAX_TIME = "StopTime_Time"
-    POST_TIME = "PostTime_Time"  # TODO: check
+    POST_TIME = "PostTime_Time"
     SIGNAL_A = "Signal_Wavelength"
     SIGNAL_B = "Signal2_Wavelength"
     SIGNAL_C = "Signal3_Wavelength"
@@ -79,7 +87,6 @@ class RegisterFlag(Enum):
     DRAW_VOLUME = "DrawVolume_Mode"
     DRAW_SPEED = "DrawSpeed_Mode"
     DRAW_OFFSET = "DrawOffset_Mode"
-    # SetObjHdrVal RCWLS1Pretreatment[1], "DrawVolume_Value", 1
     DRAW_VOLUME_VALUE = "DrawVolume_Value"
     DRAW_LOCATION = "DrawLocation"
     DRAW_LOCATION_TRAY = "DrawLocationPlus_Tray"
@@ -95,6 +102,10 @@ class RegisterFlag(Enum):
 
 @dataclass
 class Table:
+    """
+    Class for storing the keys needed to access certain register tables.
+    """
+
     register: str
     name: str
 

pychemstation/utils/tray_types.py

@@ -90,14 +90,16 @@ class Letter(Enum):
 
 @dataclass
 class FiftyFourVialPlate:
-    """
-    Class to represent the 54 vial tray. Assumes you have:
-    2 plates (P1 or P2)
-    6 rows (A B C D E F)
-    9 columns (1 2 3 4 5 6 7 8 9)
+    """Class to represent the 54 vial tray.
+
+    :param plate: one of the two, (P1 or P2)
+    :param letter: one of the rows, (A B C D E F)
+    :param num: one of the columns, (1 2 3 4 5 6 7 8 9)
 
-    valid vial locations: P1-A2, P2-F9
-    invalid vial locations: P3-A1, P1-Z3, P2-B10
+    Examples:
+    >>> from pychemstation.utils.tray_types import FiftyFourVialPlate
+    >>> FiftyFourVialPlate.from_str("P1-A2")
+    >>> FiftyFourVialPlate(plate=Plate.TWO, letter=Letter.A, num=Num.THREE)
     """
 
     plate: Plate
@@ -120,12 +122,15 @@ class FiftyFourVialPlate:
 
     @classmethod
     def from_str(cls, loc: str):
-        """
-        Converts a string representing the vial location into numerical representation for Chemstation.
+        """Converts a string representing the vial location into numerical representation for Chemstation.
 
         :param loc: vial location
         :return: `FiftyFourVialPlate` object representing the vial location
         :raises: ValueError if string is invalid tray location
+
+        Examples:
+        >>> from pychemstation.utils.tray_types import FiftyFourVialPlate
+        >>> vial_location = FiftyFourVialPlate.from_str("P2-F4")
         """
         if len(loc) != 5:
             raise ValueError(
@@ -147,15 +152,17 @@ class FiftyFourVialPlate:
 
     @classmethod
     def from_int(cls, num: int) -> Tray:
-        """
-        Converts an integer representation of a vial location to a `FiftyFourVialPlate` or `TenVialColumn` object
+        """Converts an integer representation of a vial location to a `FiftyFourVialPlate` object
 
         :param num: numerical representation of a vial location
         :return: the proper vial location object
         :raises: ValueError no matching can be made
+
+        Examples:
+        >>> vial_location = FiftyFourVialPlate.from_int(4097)
         """
         if num in range(1, 11):
-            return TenVialColumn(num)
+            return VialBar(num)
 
         row_starts = [
             # plate 1
@@ -200,9 +207,12 @@ class FiftyFourVialPlate:
         raise ValueError("Number didn't match any location. " + str(num))
 
 
-class TenVialColumn(Enum):
-    """
-    Class to represent the 10 vial locations.
+class VialBar(Enum):
+    """Class to represent the vial bar, has 10 locations.
+
+    Examples:
+    >>> vial_bar_2 = VialBar(2)
+    >>> vial_bar_10 = VialBar.TEN
     """
 
     ONE = 1
@@ -219,10 +229,12 @@ class TenVialColumn(Enum):
 
 @dataclass
 class LocationPlus:
+    """Not sure what location refers to, but part the `Draw` function for specifying an `InjectorTable`"""
+
     unit: int
     tray: int
     row: int
     col: int
 
 
-Tray = Union[FiftyFourVialPlate, TenVialColumn, LocationPlus]
+Tray = Union[FiftyFourVialPlate, VialBar, LocationPlus]

{pychemstation-0.10.7.dist-info → pychemstation-0.10.8.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.7
+Version: 0.10.8.dev1
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Project-URL: Documentation, https://pychemstation-e5a086.gitlab.io/pychemstation.html
 Project-URL: Repository, https://gitlab.com/heingroup/device-api/pychemstation
@@ -13,19 +13,13 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
 Requires-Dist: aghplctools==4.8.6
-Requires-Dist: coverage>=7.6.1
 Requires-Dist: matplotlib>=3.7.5
 Requires-Dist: pandas>=2.0.3
 Requires-Dist: pdoc>=14.7.0
 Requires-Dist: polling>=0.3.2
-Requires-Dist: pre-commit>=3.5.0
-Requires-Dist: pytest>=7.3.5
 Requires-Dist: rainbow-api>=1.0.10
 Requires-Dist: result>=0.17.0
 Requires-Dist: scipy>=1.10.1
-Requires-Dist: seabreeze>=2.9.2
-Requires-Dist: setuptools>=75.3.2
-Requires-Dist: twine>=6.1.0
 Requires-Dist: xsdata>=24.9
 Description-Content-Type: text/markdown
 

pychemstation-0.10.8.dev1.dist-info/RECORD

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pychemstation/utils/pump_types.py

@@ -1,7 +0,0 @@
-from dataclasses import dataclass
-
-
-@dataclass
-class Pump:
-    solvent: str
-    in_use: bool

pychemstation-0.10.7.dist-info/RECORD

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