Update Manual, version

.gitignore

@@ -9,4 +9,7 @@ archive/
 
 # python
 __pycache__
-venv*
+venv*
+
+#pycharm
+.idea/

doc/source/conf.py

@@ -24,9 +24,9 @@
 author = 'Robert F. DeJaco'
 
 # The short X.Y version
-version = 'v2.2.0'
+version = 'v3.0.0'
 # The full version, including alpha/beta/rc tags
-release = 'v2.2.0'
+release = 'v3.0.0'
 
 
 # -- General configuration ---------------------------------------------------

src/get_data.py

@@ -47,20 +47,29 @@ def get_C(file_name):
     Parameters
     ----------
     file_name : str
-        CSV file formatted like a 96-well plate. The top left corner looks like
-
-        +-----+---+---+
-        |  Row| 1 | 2 |
-        +=====+===+===+
-        | A   | . | . |
-        +-----+---+---+
-        | B   | . | . |
-        +-----+---+---+
-        | C   | . | . |
-        +-----+---+---+
-
-        The values are concentrations of dye in units of mol/L
-
+        CSV file containing values of
+        concentrations of dye in units of :math:`\\mu` mol/L.
+        Formatted like a 96-well plate:
+
+        +-----+---+---+---+---+---+---+---+---+---+---+---+---+
+        |  Row| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10| 11| 12|
+        +=====+===+===+===+===+===+===+===+===+===+===+===+===+
+        | A   | . | . | . | . | . | . | . | . | . | . | . | . |
+        +-----+---+---+---+---+---+---+---+---+---+---+---+---+
+        | B   | . | . | . | . | . | . | . | . | . | . | . | . |
+        +-----+---+---+---+---+---+---+---+---+---+---+---+---+
+        | C   | . | . | . | . | . | . | . | . | . | . | . | . |
+        +-----+---+---+---+---+---+---+---+---+---+---+---+---+
+        | D   | . | . | . | . | . | . | . | . | . | . | . | . |
+        +-----+---+---+---+---+---+---+---+---+---+---+---+---+
+        | E   | . | . | . | . | . | . | . | . | . | . | . | . |
+        +-----+---+---+---+---+---+---+---+---+---+---+---+---+
+        | F   | . | . | . | . | . | . | . | . | . | . | . | . |
+        +-----+---+---+---+---+---+---+---+---+---+---+---+---+
+        | G   | . | . | . | . | . | . | . | . | . | . | . | . |
+        +-----+---+---+---+---+---+---+---+---+---+---+---+---+
+        | H   | . | . | . | . | . | . | . | . | . | . | . | . |
+        +-----+---+---+---+---+---+---+---+---+---+---+---+---+
 
 
     Returns
@@ -84,15 +93,15 @@ class RawData:
     Attributes
     ----------
     F : np.ndarray
-        Fluorescence data, :math:`F_d^{t\\ell}` (see Equation 11 of main text)
+        Fluorescence data, :math:`F_d^{t,l}` (see Eq. 11)
     C : np.ndarray
-        Dye concentrations, :math:`C` (see Equation 10 of main text)
+        Dye concentrations, :math:`C` (see Eq. 10)
     B : float
         DNA concentration, :math:`B_d` in mol/L
     t : str
         Type of DNA, :math:`t`, :code:`"SS"` or :code:`"DS"` or :code:`"None"`.
     l : str
-        Replicate name, :math:`\\ell` is A, B, or C
+        Replicate name, :math:`l` is :code:`"A"`, :code:`"B"`, or code:`"C"`.
     N : int
         number of nucleobases per single strand
 
@@ -140,32 +149,32 @@ class CombinedData:
     Attributes
     ----------
     F : np.ndarray
-        Fluorescence data, :math:`\\mathbf{F}_{\\mathbf{D}}^t` in Equation (16a)
+        Fluorescence data, :math:`\\mathbf{F}_{\\mathbf{D}}^t` in Equation (13a)
     C : np.ndarray
-        Dye concentrations, :math:`\\mathbf{C}_{\\mathbf{D}}^t` in Equation (16a)
+        Dye concentrations, :math:`\\mathbf{C}_{\\mathbf{D}}^t` in Equation (13a)
     D : float
-        DNA concentration, :math:`\\mathbf{D}` in Equation (16a)
+        DNA concentration, :math:`\\mathbf{D}` in Equation (13a)
     t : str
         Type of DNA, :math:`t`, :code:`"SS"` or :code:`"DS"`
     N : int
         number of nucleobases per single strand, :math:`N`
     M_tls : np.array
-        :math:`\\mathbf{M}^\\mathrm{TLS}`, set externally, defaults to np.array([])
+        :math:`\\mathbf{M}^\\mathrm{TLS}` in Equation (18a), set externally, defaults to np.array([])
     C_hat : np.array
-        :math:`\\widehat{\\mathbf{C}}`, set externally, defaults to np.array([])
+        :math:`\\widehat{\\mathbf{C}}` in Equation (18a), set externally, defaults to np.array([])
     V_M : np.array
-        :math:`V(\\mathbf{M})` (see Section S1.2), defaults to np.array([])
+        :math:`V(\\mathbf{M})` (see section S1.3 in supporting material), defaults to np.array([])
     V_C : np.array
-        :math:`V(\\mathbf{C})` (see Section S1.2), defaults to np.array([])
+        :math:`V(\\mathbf{C})` (see section S1.3 in supporting material), defaults to np.array([])
     M_std : np.array
-        :math:`\\sqrt{V(\\mathbf{M})}` (see Section S1.2), defaults to np.array([])
+        :math:`\\sqrt{V(\\mathbf{M})}`, defaults to np.array([])
     C_std : np.array
-        :math:`\\sqrt{V(\\mathbf{C})}` (see Section S1.2), defaults to np.array([])
+        :math:`\\sqrt{V(\\mathbf{C})}`, defaults to np.array([])
 
 
     """
     def __init__(self, *replicates: typing.Tuple[RawData]) -> None:
-        """Combine replicate :math:`F` and :math:`C`
+        """Combine replicate :math:`F_d^{t,l}` and :math:`C`
 
         Parameters
         ----------
@@ -227,7 +236,7 @@ def make_subset(self, F_min):
             self.C = self.C[wells]
 
         i_T = 0
-        while (np.mean(self.F[i_T, :]) < F_min):
+        while np.mean(self.F[i_T, :]) < F_min:
             i_T += 1
 
         self.F = self.F[i_T:, :]

src/noise_removal.py

@@ -7,7 +7,7 @@ def compute_M_LS(F, C):
     Returns
     -------
     np.array
-        :math:`\\mathbf{M}^\\mathrm{LS}`, see Equation (17)
+        :math:`\\mathbf{M}^\\mathrm{LS}`, see Eq. 17.
 
     """
     return F@C/np.inner(C, C)
@@ -30,7 +30,7 @@ def compute_c_plus(F, C, M_minus, rho_squared):
     Returns
     -------
     np.ndarray
-        :math:`\\mathbf{c}_+` by Equation (S3a)
+        :math:`\\mathbf{c}_+` by Eq. S3a (see supporting material).
     """
     return (C*rho_squared + F.T@M_minus)/(rho_squared + np.inner(M_minus, M_minus))
 
@@ -48,13 +48,13 @@ def compute_M_plus(F, c_plus):
     Returns
     -------
     np.array 
-        :math:`\\mathbf{M}_{+}` by Equation (S3b)
+        :math:`\\mathbf{M}_{+}` by Eq. S3b (see supporting material).
     """
     return F@c_plus/np.inner(c_plus, c_plus)
 
 
 def predictor_corrector(F, C, rho_squared, maxiter=100000, print_iter=True):
-    """Solve Equation (18) with predictor--corrector algorithm
+    """Solve Eqs. 18 with predictor--corrector algorithm
 
     Parameters
     ----------

src/parameter_extraction.py

@@ -17,14 +17,15 @@ def calculate_relative_brightness(f_SS, f_DS):
     -------
     np.array
         Relative brightness, :math:`\\mathbf{f}^\\mathrm{DS}_j/\\mathbf{f}^\\mathrm{SS}_j` for each :math:`j` associated with SS.
+        (see Eq. 24).
 
     """
     m = f_SS.shape[0]
     return f_DS[-m:]/f_SS
 
 
 def calculate_relative_brightness_err(SS_M1, SS_M2, DS_M1, DS_M2, SS_V_M1, SS_V_M2, DS_V_M1, DS_V_M2) -> np.array:
-    """Estimate error in relative brightness, Equation (24).
+    """Estimate error in relative brightness (Eq. 24).
 
     Parameters
     ----------
@@ -78,6 +79,11 @@ def calculate_relative_brightness_err(SS_M1, SS_M2, DS_M1, DS_M2, SS_V_M1, SS_V_
 
 class Parameters:
     """Stores multiple instances of CombinedData for one DNA type
+
+    Notes
+    -----
+    :math:`\\mathbf{M}^\\mathrm{TLS}` and :math:`\\widehat{\\mathbf{C}}`
+    are defined in Eq. 18a.
     
     Attributes
     ----------
@@ -101,7 +107,7 @@ class Parameters:
     V_M1 : np.array
         :math:`V(\\mathbf{M})` associated with :math:`\\mathbf{D}=1`
     V_M2 : np.array
-        :math:`V(mathbf{M})` associated with :math:`\\mathbf{D}=2`. 
+        :math:`V(\\mathbf{M})` associated with :math:`\\mathbf{D}=2`.
         Several high temperatures are removed to reflect smaller temperature range associated with :math:`\\mathbf{D}=1`
     dT : float
         Change in temperature from one cycle to next, :math:`\\Delta T`
@@ -146,7 +152,7 @@ def __init__(self, cls1: CombinedData, cls2: CombinedData):
         assert self.N == cls2.N, "Cannot combine different DNA lengths"
 
     def get_K(self) -> np.array:
-        """Get :math:`\\mathbf{K}` from vectorized version of Equation (21)
+        """Get :math:`\\mathbf{K}` from vectorized version of Eq. 21.
 
         Returns
         -------
@@ -178,7 +184,7 @@ def get_K_std(self) -> np.array:
         return np.sqrt((DM*DM*(4*self.V_M1+ 2*self.V_M2) + DH*DH*(self.V_M1+ self.V_M2))/8/DM/DM/DM/DM)
 
     def get_f(self) -> np.array:
-        """Get :math:`\\mathbf{f}` from vectorized version of Equation (23)
+        """Get :math:`\\mathbf{f}` from vectorized version of Eq. 23.
 
         Returns
         -------
@@ -228,7 +234,7 @@ def get_f_std(self) -> np.array:
         )
 
     def get_dg(self) -> np.array:
-        """Get free energy of dye binding, :math:`\\Delta g`, vectorized version of Equation (25).
+        """Get free energy of dye binding, :math:`\\Delta g`, vectorized version of Eq. 25.
 
         Returns
         -------
@@ -239,7 +245,7 @@ def get_dg(self) -> np.array:
         return -R_kJ_molK * self.T * np.log(K/C_REF/self.N)
 
     def get_dh(self) -> np.array:
-        """Get differential enthalpy of binding, :math:`\\Delta h` as the vectorized version of Equation (26).
+        """Get differential enthalpy of binding, :math:`\\Delta h` as the vectorized version of Eq. 26.
 
         Returns
         -------
@@ -297,7 +303,7 @@ def get_dh_std(self) -> np.array:
         )
 
     def get_theta_b_all_1(self, n):
-        """Returns :math:`\\theta_{b,j,1}` in Equation (S6a) pointwise in :math:`j`
+        """Returns :math:`\\theta_{b,j,1}` from Eq. S5 pointwise in :math:`j`
         The index :math:`b` is the total number of wells.
 
         Returns

src/plot_noise_removal.py

@@ -83,7 +83,7 @@ def plot_error_C(ax, C, Chat, Chat_std=None, **kwargs):
 
 def plot_Chat_vs_C(Cs, C_hats, C_stds, fname):
     """Plot comparison between :math:`\\mathbf{C}` and :math:`\\widehat{\\mathbf{C}}`.
-    Used to plot figure 5
+    Used to plot Fig. 6
 
     Parameters
     ----------

src/plot_raw_data.py

@@ -7,7 +7,8 @@ def plot_linemap(
     cls: RawData,
     ax, colorbar=False, get_ticks=False, ordered_by_row=True
     ):
-    """Plot F vs C for various temperatures (colors)
+    """Plot :math:`F_d^t\\left(T_j, C_i\\right)` vs :math:`C_i`
+    for various temperatures :math:`T_j` (colors)
 
     Parameters
     ----------