Merge pull request #3 from liammckay19/local-mac

Local mac

.gitignore

@@ -2,3 +2,6 @@
 *.pyc
 */
 .DS_Store
+/*
+images/
+ignore/

Plate.py

@@ -0,0 +1,80 @@
+import numpy as np
+import pandas as pd
+import string
+import itertools
+import math
+
+
+class Plate():
+    def __init__(self, r, c, subwell_num):
+        """
+        General purpose plate lookup table. Converts a single number (Index) into a A01_1 format.
+        Index is ordered left-right
+
+        @param r: amount of rows
+        @param c: amount of columns
+        @param subwell_num: amount of subwells
+        """
+        self.row_num = r
+        self.col_num = c
+        self.subwell_num = subwell_num
+        self.leading_zeros = int(math.log10(round(self.col_num, 0))) + 1
+        self.zero_format = "{:0" + str(self.leading_zeros) + "d}"
+        self.matrix = self.create_plate_matrix()
+
+    def __str__(self):
+        """
+        Prints full table Pandas DataFrame as string
+        @return: Pandas DataFrame as string
+        """
+        return str(self.matrix)
+
+
+    def get_number_to_well_id(self, index):
+        """
+        Get well id (e.g. A01_1) from an Index (e.g. 1)
+        @param index: Index (counting left-right what number well is it)
+        @return: well_id
+        """
+        well_location = self.matrix[self.matrix == index].dropna(axis='index', how='all').dropna(axis='columns',
+                                                                                                 how='all')
+        if well_location.size > 0:
+            col, subcol = well_location.columns.values[0]
+            row = well_location.index.values[0]
+        else:
+            raise LookupError("%d doesn't exist in the plate" % index)
+        return row+self.zero_format.format(int(col))+"_"+str(subcol)
+
+    def create_plate_matrix(self):
+        cols = list(str(n) for n in list(range(1, self.col_num + 1)))
+        if self.row_num > len(string.ascii_letters):
+            rows = itertools.product(string.ascii_uppercase, repeat=self.row_num // 27 + 1)
+            rows = ["".join(pair) for pair in rows]
+        else:
+            rows = string.ascii_uppercase[:self.row_num]
+
+        col_list = [[n] * self.subwell_num for n in cols]
+        col_list_flat = []
+        for l in col_list:
+            for n in l:
+                col_list_flat.append(n)
+
+        multi_index_col_well_subwell_tuples = list(
+            zip(col_list_flat, [i for _ in range(self.col_num) for i in range(1, self.subwell_num + 1)]))
+        col_multindex = pd.MultiIndex.from_tuples(multi_index_col_well_subwell_tuples, names=['well', 'subwell'])
+        well_ids = [[c + self.zero_format.format(int(n)) for n in cols] for c in rows]
+        well_ids_flat = []
+        i = 1
+        for well in well_ids:
+            well_subwell_one_letter = []
+            for _ in well:
+                for subwell in range(1, self.subwell_num + 1):
+                    well_subwell_one_letter.append(i)
+                    i += 1
+            well_ids_flat.append(well_subwell_one_letter)
+
+        return pd.DataFrame(well_ids_flat,
+                            index=[c for c in rows],
+                            columns=col_multindex)
+
+