提交：初始化

.gitignore

@@ -0,0 +1,8 @@
+.idea/*
+*.
+
+__pycache__/*
+
+build/*
+dist/*
+*.egg-info/*

LICENSE

@@ -0,0 +1,127 @@
+                     木兰宽松许可证, 第2版
+
+   木兰宽松许可证， 第2版 
+   2020年1月 http://license.coscl.org.cn/MulanPSL2
+
+
+   您对“软件”的复制、使用、修改及分发受木兰宽松许可证，第2版（“本许可证”）的如下条款的约束：
+
+   0. 定义
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+   条款结束 
+
+   如何将木兰宽松许可证，第2版，应用到您的软件
+   
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+
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+
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+
+   Copyright (c) [Year] [name of copyright holder]
+   [Software Name] is licensed under Mulan PSL v2.
+   You can use this software according to the terms and conditions of the Mulan PSL v2. 
+   You may obtain a copy of Mulan PSL v2 at:
+            http://license.coscl.org.cn/MulanPSL2 
+   THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO NON-INFRINGEMENT, MERCHANTABILITY OR FIT FOR A PARTICULAR PURPOSE.  
+   See the Mulan PSL v2 for more details.  
+
+
+                     Mulan Permissive Software License，Version 2
+
+   Mulan Permissive Software License，Version 2 (Mulan PSL v2)
+   January 2020 http://license.coscl.org.cn/MulanPSL2
+
+   Your reproduction, use, modification and distribution of the Software shall be subject to Mulan PSL v2 (this License) with the following terms and conditions: 
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+
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+
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+
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+   You may obtain a copy of Mulan PSL v2 at:
+               http://license.coscl.org.cn/MulanPSL2 
+   THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO NON-INFRINGEMENT, MERCHANTABILITY OR FIT FOR A PARTICULAR PURPOSE.  
+   See the Mulan PSL v2 for more details.  

README.md

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+# tbwk-opener
+A python package to open and read tbwk files generated from the NanoDrop 2000 software.
+
+Testing: ![Python application](https://github.com/Gillingham-Lab/tbwk-opener/workflows/Python%20application/badge.svg)
+
+## Features
+This library has so far only been tested with Nucleic Acid worksheets.
+
+- Can import tbwk files to read measurements contained within the file
+- Successfully reads y- and x-values of a recorded spectrum
+- Also reports on tabled data contained in the worksheet (such as A260 for nucleic acids, 
+or direct nucleic concentration as chosen by the method)
+
+A protein worksheet (no example provided) showed similar behaviour and should work without any issues.
+
+## Installation
+
+Make sure you've installed numpy and scipy before attempting to install tbwk-opener from pip, then use:
+
+```shell script
+pip install tbwk-opener
+```
+
+
+## Usage
+
+Get all measurements from a worksheet and report on concentration using the absorption at 260 nm:
+
+```python
+from tbwk import Worksheet
+
+worksheet = Worksheet.import_worksheet("examples/nanodrop-dna-measurements-01.twbk")
+
+factor = (2.05 + 2.30)/2 # μM per absorption unit
+for measurement in worksheet:
+    print(f"{measurement.title:20}{measurement.get_absorption_at(260)*factor:.2f} μM")
+```
+
+```text
+wash                0.18 μM
+blank               0.02 μM
+BSD01               61.47 μM
+BSD01               61.11 μM
+BSD01 cntl A1       37.87 μM
+wash                0.57 μM
+BSD01 cntl A2       33.94 μM
+wash                0.27 μM
+BSD01 cntl A3       44.39 μM
+BSD01 cntl A3       0.35 μM
+BSD01 cntl A4       40.00 μM
+wash                0.05 μM
+wash                0.02 μM
+```

setup.py

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+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="tbwk-opener", # Replace with your own username
+    version="0.1.0",
+    author="Basilius Sauter",
+    author_email="basilius.sauter@gmail.com",
+    description="An tool to open tbwk files generated by NanoDrop 2000",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/Gillingham-Lab/tbwk-opener",
+    packages=setuptools.find_packages(),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Chemistry",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+        "Topic :: Utilities",
+    ],
+    python_requires='>=3.6',
+    install_requires=[
+        "numpy",
+        "scipy",
+        "defusedxml",
+    ]
+)

tbwk/Measurement.py

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+import numpy as np
+from scipy.interpolate import interp1d
+
+from tbwk.RawOpener import Block
+from tbwk.Properties import PropertyBag
+
+
+"""
+Block structure
+(all is little endian)
+
+The header of each block consists of block type (4 bytes), block size (4 bytes) and 4 empty bytes.
+
+A measurement block (151) contains 3 nested blocks. The blocks content start at 520.
+    - 152, Contains a description and the measurement name:
+        12 bytes (?)
+        1 int8 (length), usually 28
+        n char, usually "Thermo Scientific DataCarton"
+        8 bytes, usually 00 00 00 00 00 f0 3f. Might be float64 for "1.0"
+        1 int8 (length)
+        n char, contains the measurement name
+        12 bytes, usually 3 int32: [1, 1, 0]
+    - 920, a wrapper for another block.
+        12 bytes (?)
+        Then another subblock starts with FE FF FF FF, with the content starting at offset 520 again.
+        - 921
+            12 bytes
+            1 int8 (length), usually 29
+            n char, usually "Thermo Scientific UV Spectrum"
+            8 bytes, usually 00 00 00 00 00 f0 3f.
+        - 922
+            12 bytes
+            \n
+            4 bytes
+        - 930
+            12 bytes
+            Then another subblock starts with FE FF FF FF, offset at 520
+            - 931
+                12 bytes
+                1 int8 (length), usually 30
+                n char, usually "Thermo Scientific Data-Vector " (sic)
+                1 int8 (length), usually 29
+                n char, usually "SpectrumFileFormat.UVSpectrum"
+                1 int8 (length)
+                n char, measurement name again.
+                8 bytes, windows filetime, eg 97 dc af d7 2c 46 d6 01 = 2020-06-19 13:29:06.5140375 (+2)
+            - 932
+                y values.
+                y label at offset 59, containing axis label in long and short:
+                    1 int8
+                    n char
+                    1 int8
+                    n char
+                    8 bytes
+                    21 bytes
+                    1 int32 (4 bytes) indicating number of floats
+                    n float64 containing y values
+            - 932
+                x values
+                y label at offset 59, containing axis label in long and short:
+                    1 int8
+                    n char
+                    1 int8 (usually 0)
+                    n char (empty)
+                    8 bytes
+                    21 bytes
+                    1 int32 (4 bytes) indicating number of floats
+                    n float64 containing y values
+        - 990 (10X?)
+            - All contain XML data.
+        
+    - 62, content starts commonly at 520 after the block header.
+        12 bytes (?)
+        n char, XML content
+"""
+
+
+class Measurement:
+    """
+    Represents a single measurement on a NanoDrop 2000.
+
+    Use the methods of this object for the most often used parameters, or
+    access the PropertyBag to access the tabular values as set by the measurement method.
+    """
+    title: str = None
+
+    x_values: np.ndarray = None
+    x_label: str = None
+
+    y_values: np.ndarray = None
+    y_label: str = None
+
+    properties: PropertyBag = None
+
+    def __init__(self,
+                 title: str,
+                 x_values: np.ndarray,
+                 x_label: str,
+                 y_values: np.ndarray,
+                 y_label: str,
+                 properties: PropertyBag = None,
+                 ):
+        """
+
+        :param title: Title of the measurement
+        :param x_values: numpy array containing x values
+        :param x_label: label for x values
+        :param y_values: numpy array containing y values (must be equal size)
+        :param y_label: label for y values
+        :param properties: A property bag
+        """
+        assert len(x_values) == len(y_values)
+
+        self.title = title
+
+        self.x_values = x_values
+        self.x_label = x_label
+
+        self.y_values = y_values
+        self.y_label = y_label
+
+        self.properties = properties
+
+    def __repr__(self) -> str:
+        return f"<Measurement[{self.title}], {self.properties.get_method_title()}>"
+
+    def get_title(self) -> str:
+        """
+        Returns the given sample name (title) of the measurement
+        """
+        return self.title
+
+    def get_method_title(self) -> str:
+        """
+        Returns the title of the method
+        """
+        return self.properties.get_method_title()
+
+    def get_method_description(self) -> str:
+        """
+        Returns the description of the method.
+        """
+        return self.properties.get_method_description()
+
+    def get_x(self) -> np.ndarray:
+        """
+        Returns x values as a numpy array, float64
+
+        Should usually contain the measured wavelengths.
+        """
+        return self.x_values
+
+    def get_x_label(self) -> str:
+        """
+        Returns the saved label for the x-axis.
+        """
+        return self.x_label
+
+    def get_y(self) -> np.ndarray:
+        """
+        Returns y values as a numpy array, float64
+
+        Should usually contain the measured absorption.
+        :return:
+        """
+        return self.y_values
+
+    def get_y_label(self) -> str:
+        """
+        Returns the saved label for the y-axis.
+        """
+        return self.y_label
+
+    def get_property_bag(self) -> PropertyBag:
+        """
+        Returns the property bag.
+        """
+        return self.properties
+
+    def get_absorption_at(self, wavelength: float, from_spectrum=False) -> float:
+        """ Returns the absorption at a given wavelength.
+
+        If from_spectrum is set to true, the value comes always from the spectrum. If set to False, the measured
+        values are tried first. """
+
+        if from_spectrum is False:
+            wavelength_id = f"A{wavelength:.0f}"
+
+            if self.properties.has_property(wavelength_id):
+                value = self.properties.get_property(wavelength_id)
+                return value.get_value().get_value()
+
+        # Try if we find the measured value exactly
+        f = np.isin(self.x_values, wavelength, assume_unique=True)
+        result = self.y_values[f]
+
+        if len(result) == 1:
+            return result.item()
+
+        # If this does not work, we need to intrapolate
+        f = interp1d(self.x_values, self.y_values, kind="cubic")
+
+        return f(wavelength)
+
+    @classmethod
+    def from_block(cls, block):
+        assert block.type == Block.Measurement
+
+        # Create a property bag
+        properties = PropertyBag.from_xml(block.parsed_content[2].parsed_content)
+
+        # Create new measurement classes
+        ret = cls(
+            title=block.parsed_content[0].parsed_content[1].decode("utf8"),
+            x_values=block.parsed_content[1].parsed_content[2].parsed_content[2].parsed_content[3],
+            x_label=block.parsed_content[1].parsed_content[2].parsed_content[2].parsed_content[0].decode("utf8"),
+            y_values=block.parsed_content[1].parsed_content[2].parsed_content[1].parsed_content[3],
+            y_label=block.parsed_content[1].parsed_content[2].parsed_content[1].parsed_content[0].decode("utf8"),
+            properties=properties,
+        )
+
+        return ret
+
+

tbwk/Properties.py

@@ -0,0 +1,255 @@
+import numpy as np
+from typing import Dict, Optional, Tuple
+
+
+class PropertyBag:
+    """ A container for tabled properties from a measurement. """
+    method_title: str
+    method_description: str
+    method_filename: str
+
+    _properties: Dict[str, "Property"]
+
+    def __init__(self):
+        self._properties = {}
+
+    def __repr__(self) -> str:
+        return f"<PropertyBag: n={len(self._properties)}>"
+
+    def get_method_title(self) -> str:
+        """Returns the method title."""
+        return self.method_title
+
+    def get_method_description(self) -> str:
+        """Returns the method description."""
+        return self.method_description
+
+    def add_property(self, property: "Property") -> None:
+        """ Adds a property.
+        :param property: A property
+        :return:
+        """
+        self._properties[property.get_id()] = property
+
+    def has_property(self, id: str) -> bool:
+        return True if id in self._properties else False
+
+    def get_property(self, id: str) -> "Property":
+        return self._properties[id]
+
+    @classmethod
+    def from_xml(cls, xml_tree) -> "PropertyBag":
+        """ Creates a property bag from the corresponding xml tree. """
+        properties = cls()
+
+        assert xml_tree.tag == "PARAMOBJ"
+
+        # Get the spectrum results
+        spectrum_results = list(list(xml_tree)[0])[0]
+        assert spectrum_results.attrib["TYPE"] == "ParamProperties.SpectrumResults"
+
+        # Iterate over all var elements
+        for element in spectrum_results:
+            # Skip non-var elements
+            if element.tag != "VAR":
+                continue
+
+            var_name = element.attrib["NAME"]
+
+            if var_name == "m_MethodFilename":
+                properties.method_filename = element.text.strip()
+            elif var_name == "m_MethodTitle":
+                properties.method_title = element.text.strip()
+            elif var_name == "m_MethodDescription":
+                properties.method_description = element.text.strip()
+            elif var_name == "m_QuantGroups":
+                # m_QuantGroups contains all tabled measurements
+                for p in element:
+                    if p.tag != "PARAM":
+                        continue
+
+                    property = Property.from_xml(p)
+
+                    if property is not None:
+                        properties.add_property(property)
+
+        return properties
+
+
+class Property:
+    _id: str
+    _type: str
+    _value: "Value"
+    _raw: Optional["Value"]
+
+    def __init__(self,
+                 id: str,
+                 type: str,
+                 value: "Value",
+                 raw: Optional["Value"] = None,
+                 ):
+        """
+
+        :param id: Identifier, also known as the property title
+        :param type: Property type, commonly equal to the identifier
+        :param value: Property value
+        :param raw: Raw property value if found.
+        """
+        self._id = id
+        self._type = type
+        self._value = value
+        self._raw = raw
+
+    def __repr__(self) -> str:
+        return f"<Property[{self._id}]: {self._value}>"
+
+    def get_id(self) -> str:
+        return self._id
+
+    def get_type(self) -> str:
+        return self._type
+
+    def get_value(self) -> "Value":
+        return self._value
+
+    def get_raw_value(self) -> Optional["Value"]:
+        return self._raw
+
+    @classmethod
+    def from_xml(cls, xml_tree) -> Optional["Property"]:
+        property_title = None
+        property_type = None
+        property_value = None
+        property_raw = None
+
+        for var in xml_tree:
+            if var.tag != "VAR":
+                continue
+
+            if var.attrib["NAME"] == "m_Title":
+                property_title = var.text.strip()
+            elif var.attrib["NAME"] == "m_ResultType":
+                property_type = var.text.strip()
+            elif var.attrib["NAME"] == "m_QuantElements":
+                # m_QuantElements contains multiple param tags with the actual values
+                property_value, property_raw = Value.from_xml(var, property_type)
+
+        if property_value is not None:
+            property = cls(property_title, property_type, property_value, property_raw)
+        else:
+            property = None
+
+        return property
+
+
+class Value:
+    """ Represents a value """
+    _title: str
+    _digits: int
+    _value: float
+    _unit: Optional[str]
+    _factor: Optional[float]
+
+    def __init__(self,
+                 title: str,
+                 digits: int,
+                 value: float,
+                 unit: Optional[str] = None,
+                 factor: Optional[float] = None
+                 ):
+        self._title = title
+        self._digits = digits
+        self._value = value
+        self._unit = unit
+        self._factor = factor
+
+    def get_title(self) -> str:
+        return self._title
+
+    def get_digits(self) -> int:
+        return self._digits
+
+    def get_value(self) -> float:
+        return self._value
+
+    def has_unit(self) -> bool:
+        return self._unit is not None
+
+    def get_unit(self) -> Optional[str]:
+        return self._unit
+
+    def get_factor(self) -> Optional[float]:
+        return self._factor
+
+    def get_formatted_value(self) -> str:
+        """ Returns the value with the set number of digits and, if given, the unit. """
+        if self.has_unit():
+            return f"{self._value:.{self._digits}f} {self._unit}"
+        else:
+            return f"{self._value:.{self._digits}f}"
+
+    def __repr__(self):
+        return f"<Value[{self._title}]: {self._value:.{self._digits}f}>"
+
+    @classmethod
+    def from_xml(cls, xml_tree, type) -> Tuple[Optional["Value"], Optional["Value"]]:
+        value = None
+        raw_value = None
+        title = None
+        raw_title = None
+        num_digits = None
+        raw_num_digits = None
+        unit = None
+        factor = None
+
+        params = {}
+
+        for param in xml_tree:
+            if param.tag != "PARAM":
+                continue
+
+            element = {}
+            for var in param:
+                if var.tag != "VAR":
+                    continue
+
+                converted_value = var.text.strip()
+
+                if var.attrib["TYPE"] == "System.Double":
+                    converted_value = float(converted_value)
+                elif var.attrib["TYPE"] == "System.Int32":
+                    converted_value = int(converted_value)
+
+                element[var.attrib["NAME"]] = converted_value
+
+            params[element["m_ResultType"]] = element
+
+        if type in params:
+            value = params[type]["m_Value"]
+            num_digits = params[type]["m_NumDigits"]
+            title = params[type]["m_Title"]
+
+            if type + "Unit" in params:
+                unit = params[type + "Unit"]["m_Value"]
+
+            if type + "Factor" in params:
+                factor = params[type + "Factor"]["m_Value"]
+
+        if type + "Raw" in params:
+            raw_value = params[type + "Raw"]["m_Value"]
+            raw_num_digits = params[type + "Raw"]["m_NumDigits"]
+            raw_title = params[type + "Raw"]["m_Title"] + "Raw"
+
+        if value is not None:
+            tabled_value = cls(title, num_digits, value, unit, factor)
+        else:
+            tabled_value = None
+
+        if raw_title is not None:
+            raw_value = cls(raw_title, raw_num_digits, raw_value)
+        else:
+            raw_value = None
+
+        return tabled_value, raw_value
+
+

tbwk/RawOpener.py

@@ -0,0 +1,216 @@
+try:
+    import defusedxml.cElementTree as ET
+except ImportError:
+    try:
+        import defusedxml.ElementTree as ET
+    except ImportError:
+        import xml.etree.ElementTree as ET
+
+import datetime
+import numpy as np
+
+
+class Block:
+    """ Represents a "Block" in a tbwk file."""
+    Measurement = 151
+
+    head = None
+    type = None
+    parts = None
+    content = None
+    offset = None
+
+    def __init__(self, head, type, size, content, offset):
+        self.head = head
+        self.type = type
+        self.size = size
+        self.content = content
+        self.offset = offset
+
+        if type == 62:
+            self.parse_xml()
+        elif type == 63:
+            self.parse_xml()
+        elif type == 150:
+            self.parse_150()
+        elif type == 151:
+            self.parse_subblock()
+        elif type == 152:
+            self.parse_152()
+        elif type == 920:
+            self.parse_subblock()
+        elif type == 921:
+            self.parse_921()
+        elif type == 922:
+            self.parsed_content = None
+        elif type == 930:
+            self.parse_subblock()
+        elif type == 931:
+            self.parse_931()
+        elif type == 932:
+            self.parse_uv()
+        elif type == 990:
+            self.parse_xml()
+        elif type == 991:
+            self.parse_991()
+        elif type < 10000:
+            raise Exception(f"No clue what block {type} is.")
+
+    def __repr__(self):
+        # alt_types = (int.from_bytes(self.head[:1], "little"), int.from_bytes(self.head[1:2], "little"))
+        return f"<TBWK-Block {self.type} ({self.describe()}) at offset {self.offset} with size {self.size}>"
+
+    def describe(self):
+        if self.type == 63:
+            return "Main XML"
+        elif self.type == 991:
+            return self.parsed_content[0]
+        elif self.type == 151:
+            return self.parsed_content[0].parsed_content[1]
+
+    def parse_xml(self):
+        xml = ET.fromstring(self.content[12:])
+
+        self.parsed_content = xml
+
+    def parse_subblock(self):
+        content = self.content[12:]
+
+        self.parsed_content = unpack(content)
+
+    def parse_uv(self):
+        content = self.content[59:]
+        offset = 0
+
+        length1, label_long = unpack_string(content)
+        length2, label_short = unpack_string(content[offset + length1 + 1:])
+
+        offset += 1 + length1 + 1 + length2
+        offset += 8  # 8 empty bytes
+
+        offset += 21  # 4 indicating dimension again, followed by int8, then by 2x float64.
+        # First of these floats was 1 for 0 for y-axis and 1 for x-axis
+        # Second was in both cases 0. Needs more "figuring out".
+
+        number_of_values = int.from_bytes(content[offset:offset + 4], "little")
+        values = content[offset + 4:]
+
+        values = np.frombuffer(values, dtype="<f8")
+
+        self.parsed_content = (label_long, label_short, number_of_values, values)
+
+    def parse_921(self):
+        length, title = unpack_string(self.content[12:])
+
+        self.parsed_content = title
+
+    def parse_931(self):
+        offset = 12
+
+        length, blocktype = unpack_string(self.content[offset:])
+        offset += 1 + length
+
+        length, fileformat = unpack_string(self.content[offset:])
+        offset += 1 + length
+
+        length, samplename = unpack_string(self.content[offset:])
+        offset += 1 + length
+
+        sampletime = unpack_datetime(self.content[offset:])
+
+        self.parsed_content = (blocktype, fileformat, samplename, sampletime)
+
+    def parse_991(self):
+        stringLength = int.from_bytes(self.content[12:13], "little")
+        objectType = self.content[13:13 + stringLength]
+        xml = ET.fromstring(self.content[13 + stringLength:])
+
+        self.parsed_content = (objectType, xml)
+
+    def parse_150(self):
+        content = self.content[12:]
+        offset = 0
+
+        length, workbook = unpack_string(content)
+        offset += length + 1 + 8
+
+        length, workbook_type = unpack_string(content[offset:])
+        offset += length + 1 + 12
+
+        length, source = unpack_string(content[offset:])
+        offset += length + 1
+
+        length, measurement_type = unpack_string(content[offset:])
+        offset += length + 1
+
+        length, application_name = unpack_string(content[offset:])
+        offset += length + 1
+
+        length, application_version = unpack_string(content[offset:])
+        offset += length + 1
+
+        self.parsed_content = (workbook, workbook_type, source, measurement_type, application_name, application_version)
+
+    def parse_152(self):
+        content = self.content[12:]
+
+        length, blocktype = unpack_string(content)
+        length, samplename = unpack_string(content[length + 1 + 8:])
+
+        self.parsed_content = (blocktype, samplename)
+
+def unpack_string(content):
+    length = content[0]
+    string = content[1:1 + length]
+
+    return length, string
+
+
+def unpack_datetime(filetime_bin):
+    """ Converts windows file time to a datetime object.
+
+    Windows file time is a 64bit integer noted in "100 ns since January 1, 1601 UTC"
+
+    For conversion, we need to adjust the epoch first and then convert to seconds.
+
+    Source:
+    https://support.microsoft.com/en-za/help/167296/how-to-convert-a-unix-time-t-to-a-win32-filetime-or-systemtime
+
+    """
+    assert len(filetime_bin) == 8
+
+    filetime_int = int.from_bytes(filetime_bin, "little")
+
+    unixtime_in_100ns = filetime_int - 116444736000000000 # Shift the epoch to January 1, 1970 UTC
+    unixtime_in_s = unixtime_in_100ns * 0.000_000_1 # 0.000_000_1 s/100 ns
+
+    return datetime.datetime.fromtimestamp(unixtime_in_s)
+
+
+def unpack(content):
+    """ Unpacks a file or subfile and returns the individual blocks."""
+    assert content[0:4] == b"\xfe\xff\xff\xff"
+
+    header_size = int.from_bytes(content[32:36], "little")
+
+    # Unpack blocks
+    blocks = []
+    offset = 40 + header_size
+
+    while True:
+        block_head = content[offset:offset + 12]
+
+        block_type = int.from_bytes(content[offset:offset + 4], "little")
+        block_size = int.from_bytes(content[offset + 4:offset + 8], "little")
+        block_none = int.from_bytes(content[offset + 8:offset + 12], "little")
+
+        block = content[offset + 12:offset + 12 + block_size]
+
+        blocks.append(Block(block_head, block_type, block_size, block, offset))
+
+        offset += 12 + block_size
+
+        if offset == len(content):
+            break
+
+    return blocks

tbwk/Worksheet.py

@@ -0,0 +1,60 @@
+from typing import List
+from tbwk.RawOpener import unpack, Block
+from tbwk.Measurement import Measurement
+
+
+class Worksheet:
+    measurements: List[Measurement] = None
+
+    def __init__(self):
+        self.measurements = []
+
+    def __len__(self) -> int:
+        """ Returns the number of measurements within the worksheet. """
+        return len(self.measurements)
+
+    def __iter__(self):
+        for measurement in self.measurements:
+            yield measurement
+
+    def add_measurement(self, measurement: Measurement) -> None:
+        """
+        Adds a measurement to the worksheet
+
+        :param measurement:
+        :return:
+        """
+        self.measurements.append(measurement)
+
+
+def import_worksheet(filename: str) -> Worksheet:
+    """
+    imports a given filename and creates a tbwk.Worksheet object.
+
+    :param filename:
+    :return:
+    """
+
+    with open(filename, "rb") as fh:
+        content = fh.read()
+
+    if content is None:
+        raise FileNotFoundError(f"File {filename} was not found.")
+
+    # Unpack the file
+    blocks = unpack(content)
+
+    # Start loading the worksheet with found data.
+    worksheet = Worksheet()
+
+    # Add measurements
+    for block in blocks:
+        if block.type == Block.Measurement:
+            # Add a measurement block
+            measurement = Measurement.from_block(block)
+
+            worksheet.add_measurement(measurement)
+        # ToDo: Import data from other blocks, too.
+
+    return worksheet
+

test.py

@@ -0,0 +1,8 @@
+from tbwk import Worksheet
+
+worksheet = Worksheet.import_worksheet("examples/nanodrop-dna-measurements-01.twbk")
+
+factor = (2.05 + 2.30)/2 # μM per absorption unit
+for measurement in worksheet:
+    print(f"{measurement.title:20}{measurement.get_absorption_at(260)*factor:.2f} μM")
+

tests/test_NucleicAcid_Worksheet.py

@@ -0,0 +1,75 @@
+import unittest
+
+from tbwk import Worksheet
+
+
+class NucleicAcidWorksheetTestCase(unittest.TestCase):
+    def setUp(self):
+        filenames = [
+            "examples/nanodrop-dna-measurements-01.twbk",
+            "examples/nanodrop-dna-measurements-02.twbk",
+        ]
+
+        worksheets = []
+
+        for file in filenames:
+            worksheets.append(Worksheet.import_worksheet(file))
+
+        self.worksheets = worksheets
+
+    def test_number_of_measurements(self):
+        number_of_experiments = [
+            13, 6,
+        ]
+
+        for i in range(len(self.worksheets)):
+            should = number_of_experiments[i]
+            actual = len(self.worksheets[i])
+
+            self.assertEqual(should, actual)
+
+    def test_measurements_titles(self):
+        measurement_titles = [
+            ["wash", "blank", "BSD01", "BSD01", "BSD01 cntl A1", "wash", "BSD01 cntl A2",
+             "wash", "BSD01 cntl A3", "BSD01 cntl A3", "BSD01 cntl A4", "wash", "wash"],
+            ["blank", "blank", "CF2", "CF1", "wash", "wash"],
+        ]
+
+        for i in range(len(self.worksheets)):
+            worksheet = self.worksheets[i]
+
+            for j in range(len(worksheet)):
+                should = measurement_titles[i][j]
+                actual = worksheet.measurements[j].title
+
+                self.assertEqual(should, actual)
+
+    def test_measurements_axes(self):
+        x_should = "Wavelength (nm)"
+        y_should = "10mm Absorbance"
+
+        for i in range(len(self.worksheets)):
+            worksheet = self.worksheets[i]
+
+            for j in range(len(worksheet)):
+                x_actual = worksheet.measurements[j].x_label
+                y_actual = worksheet.measurements[j].y_label
+
+                self.assertEqual(x_should, x_actual, msg="X-Axis label not matching.")
+                self.assertEqual(y_should, y_actual, msg="Y-Axis label not matching.")
+
+    def test_absorption_at_wavelength(self):
+        measurement_values = [
+            [0.08149, 0.00837, 28.260080, 28.09851, 17.41371, 0.26109, 15.60493, 0.12195, 20.41074, 0.15920,
+             18.39145, 0.024534, 0.01116],
+            [0.87528, 0.00378, 7.41706, 6.30852, 0.047512, 0.03308],
+        ]
+
+        for i in range(len(self.worksheets)):
+            worksheet = self.worksheets[i]
+
+            for j in range(len(worksheet)):
+                actual = worksheet.measurements[j].get_absorption_at(260)
+                should = measurement_values[i][j]
+
+                self.assertAlmostEqual(actual, should, 4)

tests/test_Properties_Value.py

@@ -0,0 +1,36 @@
+import unittest
+
+from tbwk.Properties import Value
+
+class PropertiesValueTestCase(unittest.TestCase):
+    test_parameters = [
+        {"title": "A title", "digits": 3, "value": 1.26391, "unit": "mg/mL", "factor": 33.0,}
+    ]
+
+    def test_getters(self):
+        for i in range(len(self.test_parameters)):
+            parameters = self.test_parameters[i]
+
+            with self.subTest(i=i, parameters=parameters):
+                value = Value(**parameters)
+
+                self.assertEqual(parameters["title"], value.get_title())
+                self.assertEqual(parameters["digits"], value.get_digits())
+                self.assertAlmostEqual(parameters["value"], value.get_value(), value.get_digits())
+                self.assertEqual(parameters["unit"], value.get_unit())
+                self.assertAlmostEqual(parameters["factor"], value.get_factor(), 3)
+
+    def test_if_value_gets_formatted_as_expected(self):
+        expected = [
+            "1.264 mg/mL",
+        ]
+
+        for i in range(len(self.test_parameters)):
+            parameters = self.test_parameters[i]
+            should = expected[i]
+
+            with self.subTest(i=i, parameters=parameters):
+                value = Value(**parameters)
+                actual = value.get_formatted_value()
+
+                self.assertEqual(should, actual)