BUG CSV: fix problem with trailing whitespace in skipped rows, issues 8661, 8679

Scott E Lasley · Scott Lasley · commit 6bf83c5dc575 · 2014-11-26T18:00:00.000-05:00
ENH CSV: Reduce memory usage when skiprows is an integer in read_csv, issue 8681
diff --git a/doc/source/whatsnew/v0.15.2.txt b/doc/source/whatsnew/v0.15.2.txt
@@ -74,6 +74,7 @@ Enhancements
 
 Performance
 ~~~~~~~~~~~
+- Reduce memory usage when skiprows is an integer in read_csv (:issue:`8681`)
 
 .. _whatsnew_0152.experimental:
 
@@ -155,3 +156,4 @@ Bug Fixes
   of the level names are numbers (:issue:`8584`).
 - Bug in ``MultiIndex`` where ``__contains__`` returns wrong result if index is
   not lexically sorted or unique (:issue:`7724`)
+- BUG CSV: fix problem with trailing whitespace in skipped rows, (:issue:`8679`), (:issue:`8661`)
diff --git a/pandas/io/tests/test_parsers.py b/pandas/io/tests/test_parsers.py
@@ -3048,6 +3048,29 @@ def test_comment_skiprows(self):
         df = self.read_csv(StringIO(data), comment='#', skiprows=4)
         tm.assert_almost_equal(df.values, expected)
 
+    def test_trailing_spaces(self):
+        data = """skip
+random line with trailing spaces    
+skip
+1,2,3
+1,2.,4.
+random line with trailing tabs\t\t\t
+     
+5.,NaN,10.0
+"""
+        expected = pd.DataFrame([[1., 2., 4.],
+                    [5., np.nan, 10.]])
+        # this should ignore six lines including lines with trailing 
+        # whitespace and blank lines.  issues 8661, 8679
+        df = self.read_csv(StringIO(data.replace(',', '  ')), 
+                           header=None, delim_whitespace=True,
+                           skiprows=[0,1,2,3,5,6], skip_blank_lines=True)
+        tm.assert_frame_equal(df, expected)
+        df = self.read_table(StringIO(data.replace(',', '  ')), 
+                             header=None, delim_whitespace=True,
+                             skiprows=[0,1,2,3,5,6], skip_blank_lines=True)
+        tm.assert_frame_equal(df, expected)
+
     def test_comment_header(self):
         data = """# empty
 # second empty line
diff --git a/pandas/parser.pyx b/pandas/parser.pyx
@@ -86,6 +86,7 @@ cdef extern from "parser/tokenizer.h":
         EAT_COMMENT
         EAT_LINE_COMMENT
         WHITESPACE_LINE
+        SKIP_LINE
         FINISHED
 
     enum: ERROR_OVERFLOW
@@ -158,6 +159,7 @@ cdef extern from "parser/tokenizer.h":
         int header_end # header row end
 
         void *skipset
+        int64_t skip_first_N_rows
         int skip_footer
         double (*converter)(const char *, char **, char, char, char, int)
 
@@ -181,6 +183,8 @@ cdef extern from "parser/tokenizer.h":
     void parser_free(parser_t *self) nogil
     int parser_add_skiprow(parser_t *self, int64_t row)
 
+    int parser_set_skipfirstnrows(parser_t *self, int64_t nrows)
+
     void parser_set_default_options(parser_t *self)
 
     int parser_consume_rows(parser_t *self, size_t nrows)
@@ -524,10 +528,10 @@ cdef class TextReader:
 
     cdef _make_skiprow_set(self):
         if isinstance(self.skiprows, (int, np.integer)):
-            self.skiprows = range(self.skiprows)
-
-        for i in self.skiprows:
-            parser_add_skiprow(self.parser, i)
+            parser_set_skipfirstnrows(self.parser, self.skiprows)
+        else:
+            for i in self.skiprows:
+                parser_add_skiprow(self.parser, i)
 
     cdef _setup_parser_source(self, source):
         cdef:
diff --git a/pandas/src/parser/tokenizer.c b/pandas/src/parser/tokenizer.c
@@ -156,6 +156,7 @@ void parser_set_default_options(parser_t *self) {
     self->thousands = '\0';
 
     self->skipset = NULL;
+    self-> skip_first_N_rows = -1;
     self->skip_footer = 0;
 }
 
@@ -444,21 +445,17 @@ static int end_line(parser_t *self) {
         }
     }
 
-    if (self->skipset != NULL) {
-        k = kh_get_int64((kh_int64_t*) self->skipset, self->file_lines);
-
-        if (k != ((kh_int64_t*)self->skipset)->n_buckets) {
-            TRACE(("Skipping row %d\n", self->file_lines));
-            // increment file line count
-            self->file_lines++;
-
-            // skip the tokens from this bad line
-            self->line_start[self->lines] += fields;
+    if (self->state == SKIP_LINE) {
+        TRACE(("Skipping row %d\n", self->file_lines));
+        // increment file line count
+        self->file_lines++;
+        
+        // skip the tokens from this bad line
+        self->line_start[self->lines] += fields;
 
-            // reset field count
-            self->line_fields[self->lines] = 0;
-            return 0;
-        }
+        // reset field count
+        self->line_fields[self->lines] = 0;
+        return 0;
     }
 
     /* printf("Line: %d, Fields: %d, Ex-fields: %d\n", self->lines, fields, ex_fields); */
@@ -556,6 +553,15 @@ int parser_add_skiprow(parser_t *self, int64_t row) {
     return 0;
 }
 
+int parser_set_skipfirstnrows(parser_t *self, int64_t nrows) {
+    // self->file_lines is zero based so subtract 1 from nrows
+    if (nrows > 0) {
+        self->skip_first_N_rows = nrows - 1;
+    }
+
+    return 0;
+}
+
 static int parser_buffer_bytes(parser_t *self, size_t nbytes) {
     int status;
     size_t bytes_read;
@@ -656,6 +662,15 @@ typedef int (*parser_op)(parser_t *self, size_t line_limit);
     TRACE(("datapos: %d, datalen: %d\n", self->datapos, self->datalen));
 
 
+int skip_this_line(parser_t *self, int64_t rownum) {
+    if (self->skipset != NULL) {
+        return ( kh_get_int64((kh_int64_t*) self->skipset, self->file_lines) != 
+                 ((kh_int64_t*)self->skipset)->n_buckets );
+    }
+    else {
+        return ( rownum <= self->skip_first_N_rows );
+    }
+}
 
 int tokenize_delimited(parser_t *self, size_t line_limit)
 {
@@ -688,10 +703,25 @@ int tokenize_delimited(parser_t *self, size_t line_limit)
 
         switch(self->state) {
 
+        case SKIP_LINE:
+//            TRACE(("tokenize_delimited SKIP_LINE %c, state %d\n", c, self->state));
+            if (c == '\n') {
+                END_LINE();
+            }
+            break;
+
         case START_RECORD:
             // start of record
-
-            if (c == '\n') {
+            if (skip_this_line(self, self->file_lines)) {
+                if (c == '\n') {
+                    END_LINE()
+                }
+                else {
+                    self->state = SKIP_LINE;
+                }
+                break;
+            }
+            else if (c == '\n') {
                 // \n\r possible?
                 if (self->skip_empty_lines)
                 {
@@ -1006,9 +1036,26 @@ int tokenize_delim_customterm(parser_t *self, size_t line_limit)
                self->state));
 
         switch(self->state) {
+
+        case SKIP_LINE:
+//            TRACE(("tokenize_delim_customterm SKIP_LINE %c, state %d\n", c, self->state));
+            if (c == self->lineterminator) {
+                END_LINE();
+            }
+            break;
+
         case START_RECORD:
             // start of record
-            if (c == self->lineterminator) {
+            if (skip_this_line(self, self->file_lines)) {
+                if (c == self->lineterminator) {
+                    END_LINE()
+                }
+                else {
+                    self->state = SKIP_LINE;
+                }
+                break;
+            }
+            else if (c == self->lineterminator) {
                 // \n\r possible?
                 if (self->skip_empty_lines)
                 {
@@ -1252,6 +1299,14 @@ int tokenize_whitespace(parser_t *self, size_t line_limit)
                self->state));
 
         switch(self->state) {
+
+        case SKIP_LINE:
+//            TRACE(("tokenize_whitespace SKIP_LINE %c, state %d\n", c, self->state));
+            if (c == '\n') {
+                END_LINE();
+            }
+            break;
+
         case WHITESPACE_LINE:
             if (c == '\n') {
                 self->file_lines++;
@@ -1283,9 +1338,17 @@ int tokenize_whitespace(parser_t *self, size_t line_limit)
 
         case START_RECORD:
             // start of record
-            if (c == '\n') {
-                // \n\r possible?
+            if (skip_this_line(self, self->file_lines)) {
+                if (c == '\n') {
+                    END_LINE()
+                }
+                else {
+                    self->state = SKIP_LINE;
+                }
+                break;
+            } else  if (c == '\n') {
                 if (self->skip_empty_lines)
+                // \n\r possible?
                 {
                     self->file_lines++;
                 }
diff --git a/pandas/src/parser/tokenizer.h b/pandas/src/parser/tokenizer.h
@@ -127,6 +127,7 @@ typedef enum {
     EAT_COMMENT,
     EAT_LINE_COMMENT,
     WHITESPACE_LINE,
+    SKIP_LINE,
     FINISHED
 } ParserState;
 
@@ -203,6 +204,7 @@ typedef struct parser_t {
     int header_end;   // header row end
 
     void *skipset;
+    int64_t skip_first_N_rows;
     int skip_footer;
     double (*converter)(const char *, char **, char, char, char, int);
 
@@ -240,6 +242,8 @@ int parser_trim_buffers(parser_t *self);
 
 int parser_add_skiprow(parser_t *self, int64_t row);
 
+int parser_set_skipfirstnrows(parser_t *self, int64_t nrows);
+
 void parser_free(parser_t *self);
 
 void parser_set_default_options(parser_t *self);
diff --git a/vb_suite/io_bench.py b/vb_suite/io_bench.py
@@ -21,6 +21,22 @@
 read_csv_standard = Benchmark("read_csv('__test__.csv')", setup1,
                               start_date=datetime(2011, 9, 15))
 
+#----------------------------------
+# skiprows
+
+setup1 = common_setup + """
+index = tm.makeStringIndex(20000)
+df = DataFrame({'float1' : randn(20000),
+                'float2' : randn(20000),
+                'string1' : ['foo'] * 20000,
+                'bool1' : [True] * 20000,
+                'int1' : np.random.randint(0, 200000, size=20000)},
+               index=index)
+df.to_csv('__test__.csv')
+"""
+
+read_csv_skiprows = Benchmark("read_csv('__test__.csv', skiprows=10000)", setup1,
+                              start_date=datetime(2011, 9, 15))
 
 #----------------------------------------------------------------------
 # write_csv
