From a8d39ae7d340ae3faab201d48592c5f1b169317a Mon Sep 17 00:00:00 2001
From: Skoricius <lukaskoric32@gmail.com>
Date: Tue, 30 Apr 2024 10:15:29 +0200
Subject: [PATCH] removing unnecessary changes

---
 f3ast/stream_builder.py | 59 +++++------------------------------------
 1 file changed, 7 insertions(+), 52 deletions(-)

diff --git a/f3ast/stream_builder.py b/f3ast/stream_builder.py
index aecef2e..822589d 100644
--- a/f3ast/stream_builder.py
+++ b/f3ast/stream_builder.py
@@ -8,8 +8,6 @@
 
 class StreamBuilder:
     """Builds the stream using the microscope settings.
-
-
     Attributes:
         dwells_slices (list of (n,3) arrays): Specifying per layer dwells (t, x, y)
         addressable_pixels (list of two int): Microscope addressable pixels.
@@ -43,10 +41,8 @@ def __init__(
     @classmethod
     def from_model(cls, model, **kwargs):
         """Creates the class from the model. Internally creates the DwellSolver and solves for dwells.
-
         Args:
             model (Model): Class defining the growth model.
-
         Returns:
             tuple:
                 stream_builder (StreamBuilder), dwell_solver (DwellSolver)
@@ -66,10 +62,8 @@ def ppn(self):
 
     def get_stream(self, centre=False):
         """Builds the stream object from the calculated dwells
-
         Args:
             centre (bool, optional): Wether to centre the stream on the screen. Defaults to False.
-
         Returns:
             Stream:
         """
@@ -89,8 +83,8 @@ def get_stream(self, centre=False):
         return stream
 
     def get_stream_dwells(self):
-        """Gets the stream dwells by splitting and ordering them appropriately. Also converts x, y in pixels and gets rid of small dwells.
-
+        """Gets the stream dwells by splitting and ordering them appropriately.
+        Also converts x, y in pixels and gets rid of small dwells.
         Returns:
             (n,3) array: Array of dwells.
         """
@@ -124,56 +118,17 @@ def get_stream_dwells(self):
 
     @staticmethod
     def split_dwells(dwells, max_dwt):
-        """Takes a matrix of dwells and splits them so that none of them exceeds the max dwell time. Returns a list of N_reps items which are all the split dwells.
-
+        """Takes a matrix of dwells and splits them so that none of them
+        exceeds the max dwell time. Returns a list of N_reps items which are
+        all the split dwells.
         Args:
             dwells ((n,3) array): Array of dwells
             max_dwt (float): Maximum allowed dwell time.
-
         Returns:
-            list: List of equal (n,3) arrays that when summed correspond to the dwells.
+            list: List of equal (n,3) arrays that when summed correspond to
+            the dwells.
         """
         n_splits = int(np.ceil(np.max(dwells[:, 0]) / max_dwt))
         dwells_reduced = dwells.copy()
         dwells_reduced[:, 0] = dwells_reduced[:, 0] / n_splits
         return [dwells_reduced for i in range(n_splits)]
-
-
-def stream_exp_correction_with_z(
-    struct, settings, GR0=40e-3, doubling_length=500.0, sigma=4.2
-):
-    """
-    Returns stream model with exponential correction over structure height.
-    Might be useful for stl files with disconnected components, which leads to a breakdown of the DDModel.
-
-    Takes initial growth rate/time from GR, and doubles dwell time over the length scale of doubling_length.    Doubling_length needs to be determined experimentally, e.g., from pitch of periodic structures over heights.
-
-    Args:
-        struct: structure
-        GR: growth rate in um/s
-        doubling_length: in nm, length over which deposition time doubles
-        sigma: in nm, deposit width
-    Returns:
-        stream_builder, dwell_solver
-    """
-
-    from . import StreamBuilder
-    from .deposit_model import RRLModel
-
-    # solve dwells for k=0 and take the data as input to create streams
-    model = RRLModel(struct, GR0, sigma)
-    stream_builder, dwell_solver = StreamBuilder.from_model(
-        model, **settings["stream_builder"]
-    )
-
-    # calculate times in dependence of z from dwell matrix
-    dwell_matrix = dwell_solver.get_dwells_matrix()  # t, x, y, z (n, 4)
-    dwell_matrix[:, 0] = np.mean(dwell_matrix[:, 0]) * np.power(
-        2.0, dwell_matrix[:, 3] / doubling_length
-    )
-    # transform dwell matrix to dwell slices stacked along z, and overwrite class property
-    stream_builder.dwells_slices = np.split(
-        dwell_matrix, np.unique(dwell_matrix[:, -1], return_index=True)[-1][1:]
-    )
-
-    return stream_builder, dwell_solver